Starting phenix.real_space_refine on Sun May 3 19:19:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hej_52078/05_2026/9hej_52078.map" } resolution = 2.82 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= 0.014 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 Ca 9 9.91 5 Fe 2 7.16 5 S 133 5.16 5 C 9441 2.51 5 N 2682 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15177 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5661 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 23, 'TRANS': 724} Chain breaks: 1 Chain: "B" Number of atoms: 4780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4780 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 19, 'TRANS': 611} Chain breaks: 1 Chain: "D" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "E" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1084 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "F" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 34 Unusual residues: {' CA': 6, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15177 At special positions: 0 Unit cell: (98.176, 138.112, 191.36, 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) Fe 2 26.01 Ca 9 19.99 S 133 16.00 O 2910 8.00 N 2682 7.00 C 9441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.04 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 972 " distance=2.03 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1028 " distance=2.03 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.04 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 452 " distance=2.04 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 547 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 818 " distance=2.02 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 869 " distance=2.03 Simple disulfide: pdb=" SG CYS B 864 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 895 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 250 " - pdb=" SG CYS F 281 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 322 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1201 " - " ASN A 445 " " NAG A1202 " - " ASN A1027 " " NAG B1201 " - " ASN B 320 " " NAG C 1 " - " ASN A 320 " " NAG F 401 " - " ASN F 182 " " NAG H 1 " - " ASN B 767 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 683.9 milliseconds 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 33 sheets defined 26.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.654A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.668A pdb=" N CYS A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.596A pdb=" N ASP A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.729A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.976A pdb=" N PHE A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.694A pdb=" N GLN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.588A pdb=" N CYS A 967 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 968 " --> pdb=" O GLN A 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 403 through 415 removed outlier: 4.385A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.987A pdb=" N ASP B 572 " --> pdb=" O HIS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.744A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.520A pdb=" N HIS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.858A pdb=" N ASP B 813 " --> pdb=" O HIS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 removed outlier: 4.015A pdb=" N VAL B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'D' and resid 4 through 19 Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.554A pdb=" N TYR D 43 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 96 through 114 removed outlier: 3.909A pdb=" N LYS D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 139 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 17 through 19 No H-bonds generated for 'chain 'E' and resid 17 through 19' Processing helix chain 'E' and resid 23 through 36 Processing helix chain 'E' and resid 37 through 47 removed outlier: 4.047A pdb=" N GLU E 44 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY E 47 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 58 through 77 removed outlier: 3.617A pdb=" N ALA E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 101 through 120 removed outlier: 3.844A pdb=" N ARG E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 144 removed outlier: 4.442A pdb=" N HIS E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 162 removed outlier: 4.278A pdb=" N ALA F 159 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Proline residue: F 160 - end of helix Processing helix chain 'F' and resid 246 through 256 Processing helix chain 'F' and resid 336 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 4.085A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 255 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 4.085A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 172 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 183 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TRP A 222 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR A 182 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.586A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.586A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS A 327 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 380 removed outlier: 4.519A pdb=" N GLY A 378 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 383 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 380 removed outlier: 4.519A pdb=" N GLY A 378 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 383 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 482 removed outlier: 6.944A pdb=" N GLY A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE A 527 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 576 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 482 removed outlier: 7.363A pdb=" N VAL A 491 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE A 502 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP A 541 " --> pdb=" O TRP A 499 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 501 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 586 removed outlier: 3.654A pdb=" N VAL A 680 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 681 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 583 through 586 removed outlier: 5.755A pdb=" N VAL A 596 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 600 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN A 644 " --> pdb=" O TRP A 604 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.989A pdb=" N SER A 823 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 838 " --> pdb=" O THR A 827 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 931 through 932 removed outlier: 3.573A pdb=" N VAL A1026 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 931 through 932 removed outlier: 6.401A pdb=" N VAL A 942 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 953 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP A 992 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR A 952 " --> pdb=" O TRP A 992 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.653A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 277 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 363 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.653A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS B 327 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 376 removed outlier: 4.193A pdb=" N GLU B 372 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 389 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 374 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR B 471 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 372 through 376 removed outlier: 4.193A pdb=" N GLU B 372 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 389 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 374 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU B 437 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 477 through 480 removed outlier: 3.552A pdb=" N GLY B 489 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 575 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 removed outlier: 5.931A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 584 through 586 removed outlier: 3.764A pdb=" N ARG B 584 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B 596 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TRP B 604 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TRP B 646 " --> pdb=" O TRP B 604 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER B 606 " --> pdb=" O TRP B 646 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.602A pdb=" N ILE B 681 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 649 through 650 removed outlier: 3.501A pdb=" N THR B 665 " --> pdb=" O MET B 649 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.629A pdb=" N ARG B 720 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY B 815 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA B 768 " --> pdb=" O GLY B 815 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 817 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.629A pdb=" N ARG B 720 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 732 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 743 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TRP B 782 " --> pdb=" O TRP B 740 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 742 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 831 through 834 removed outlier: 4.784A pdb=" N ARG B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER B 828 " --> pdb=" O ARG B 832 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 831 through 834 removed outlier: 4.784A pdb=" N ARG B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER B 828 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 839 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP B 889 " --> pdb=" O TRP B 847 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR B 849 " --> pdb=" O TRP B 889 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 48 through 49 removed outlier: 3.510A pdb=" N THR F 67 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AD4, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AD5, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.681A pdb=" N LYS F 238 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL F 219 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N HIS F 303 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER F 223 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA F 299 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 314 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL F 302 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA F 312 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 329 " --> pdb=" O SER F 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 170 through 172 removed outlier: 4.208A pdb=" N LEU F 164 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU F 190 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL F 177 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS F 192 " --> pdb=" O GLU F 175 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1461 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: 3.15 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 5773 1.38 - 1.55: 9558 1.55 - 1.72: 39 1.72 - 1.89: 155 1.89 - 2.05: 8 Bond restraints: 15533 Sorted by residual: bond pdb=" O1 OXY D 202 " pdb=" O2 OXY D 202 " ideal model delta sigma weight residual 1.109 1.208 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O1 OXY E 202 " pdb=" O2 OXY E 202 " ideal model delta sigma weight residual 1.109 1.208 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N MET A 884 " pdb=" CA MET A 884 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.17e-02 7.31e+03 6.01e+00 bond pdb=" N LEU B 371 " pdb=" CA LEU B 371 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.50e+00 bond pdb=" N LEU A 460 " pdb=" CA LEU A 460 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.32e-02 5.74e+03 4.89e+00 ... (remaining 15528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 20489 1.93 - 3.86: 492 3.86 - 5.79: 83 5.79 - 7.71: 16 7.71 - 9.64: 7 Bond angle restraints: 21087 Sorted by residual: angle pdb=" CA LYS A 874 " pdb=" CB LYS A 874 " pdb=" CG LYS A 874 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" CA VAL A 426 " pdb=" CB VAL A 426 " pdb=" CG1 VAL A 426 " ideal model delta sigma weight residual 110.40 116.59 -6.19 1.70e+00 3.46e-01 1.32e+01 angle pdb=" C CYS A 567 " pdb=" N SER A 568 " pdb=" CA SER A 568 " ideal model delta sigma weight residual 121.54 114.68 6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N SER F 113 " pdb=" CA SER F 113 " pdb=" C SER F 113 " ideal model delta sigma weight residual 107.48 115.67 -8.19 2.29e+00 1.91e-01 1.28e+01 angle pdb=" CB LYS A 874 " pdb=" CG LYS A 874 " pdb=" CD LYS A 874 " ideal model delta sigma weight residual 111.30 119.40 -8.10 2.30e+00 1.89e-01 1.24e+01 ... (remaining 21082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8190 17.95 - 35.89: 814 35.89 - 53.84: 212 53.84 - 71.78: 52 71.78 - 89.73: 23 Dihedral angle restraints: 9291 sinusoidal: 3789 harmonic: 5502 Sorted by residual: dihedral pdb=" CB CYS A 835 " pdb=" SG CYS A 835 " pdb=" SG CYS A 869 " pdb=" CB CYS A 869 " ideal model delta sinusoidal sigma weight residual -86.00 -9.06 -76.94 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS A 411 " pdb=" SG CYS A 411 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual 93.00 168.45 -75.45 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A 503 " pdb=" SG CYS A 503 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual 93.00 164.99 -71.99 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 9288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1976 0.072 - 0.144: 271 0.144 - 0.216: 20 0.216 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 2269 Sorted by residual: chirality pdb=" CB ILE B 781 " pdb=" CA ILE B 781 " pdb=" CG1 ILE B 781 " pdb=" CG2 ILE B 781 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 445 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASP A1007 " pdb=" N ASP A1007 " pdb=" C ASP A1007 " pdb=" CB ASP A1007 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2266 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1006 " 0.041 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP A1006 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A1006 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A1006 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1006 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1006 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1006 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1006 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1006 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1006 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 612 " 0.025 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A 612 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 612 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 612 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 612 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 612 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 612 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 612 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 612 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 612 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 87 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C LEU D 87 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU D 87 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS D 88 " -0.015 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1634 2.75 - 3.28: 14680 3.28 - 3.82: 24099 3.82 - 4.36: 28779 4.36 - 4.90: 50077 Nonbonded interactions: 119269 Sorted by model distance: nonbonded pdb=" N GLU A 857 " pdb=" OE1 GLU A 857 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP B 746 " pdb="CA CA B1204 " model vdw 2.209 2.510 nonbonded pdb=" OG SER A 508 " pdb=" OE1 GLU A 510 " model vdw 2.210 3.040 nonbonded pdb=" O GLU B 911 " pdb=" NH1 ARG B 913 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP B 784 " pdb="CA CA B1203 " model vdw 2.236 2.510 ... (remaining 119264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' } 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: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 0.004 0.138 15597 Z= 0.170 Angle : 0.746 13.828 21219 Z= 0.385 Chirality : 0.049 0.359 2269 Planarity : 0.005 0.094 2726 Dihedral : 15.794 89.727 5617 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.92 % Allowed : 18.50 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 1945 helix: 1.24 (0.27), residues: 387 sheet: -1.19 (0.32), residues: 243 loop : -1.21 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 59 TYR 0.024 0.002 TYR B 580 PHE 0.046 0.002 PHE B 821 TRP 0.078 0.002 TRP A1006 HIS 0.016 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00397 (15533) covalent geometry : angle 0.72854 (21087) SS BOND : bond 0.00323 ( 54) SS BOND : angle 2.12401 ( 108) hydrogen bonds : bond 0.21679 ( 503) hydrogen bonds : angle 7.82237 ( 1461) Misc. bond : bond 0.09752 ( 2) link_BETA1-4 : bond 0.00675 ( 2) link_BETA1-4 : angle 2.69551 ( 6) link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 2.31012 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.616 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: A 539 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 600 THR cc_start: 0.7175 (p) cc_final: 0.6929 (t) REVERT: B 911 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6934 (tm-30) REVERT: E 123 PHE cc_start: 0.8628 (t80) cc_final: 0.8417 (t80) REVERT: F 176 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8461 (ptmm) REVERT: F 295 ASP cc_start: 0.8487 (m-30) cc_final: 0.8275 (m-30) outliers start: 31 outliers final: 23 residues processed: 304 average time/residue: 0.6184 time to fit residues: 207.2224 Evaluate side-chains 300 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 286 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 454 ASN A 946 HIS D 79 ASN E 3 HIS ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.179308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148687 restraints weight = 23164.340| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.58 r_work: 0.3794 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 15597 Z= 0.168 Angle : 0.655 9.590 21219 Z= 0.334 Chirality : 0.046 0.266 2269 Planarity : 0.005 0.063 2726 Dihedral : 7.953 83.361 2300 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.17 % Allowed : 16.64 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 1945 helix: 1.55 (0.27), residues: 402 sheet: -0.74 (0.31), residues: 268 loop : -1.02 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 376 TYR 0.018 0.001 TYR B 580 PHE 0.017 0.001 PHE A 650 TRP 0.021 0.001 TRP A 612 HIS 0.008 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00399 (15533) covalent geometry : angle 0.64519 (21087) SS BOND : bond 0.00361 ( 54) SS BOND : angle 1.04084 ( 108) hydrogen bonds : bond 0.04412 ( 503) hydrogen bonds : angle 5.56040 ( 1461) Misc. bond : bond 0.09594 ( 2) link_BETA1-4 : bond 0.00603 ( 2) link_BETA1-4 : angle 3.33261 ( 6) link_NAG-ASN : bond 0.00462 ( 6) link_NAG-ASN : angle 2.73441 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 0.515 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: A 162 THR cc_start: 0.9041 (p) cc_final: 0.8794 (t) REVERT: A 175 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7849 (ttpp) REVERT: A 426 VAL cc_start: 0.8807 (t) cc_final: 0.8555 (t) REVERT: B 600 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6759 (t) REVERT: B 638 PHE cc_start: 0.7254 (m-80) cc_final: 0.6624 (m-80) REVERT: B 884 MET cc_start: 0.5078 (mmm) cc_final: 0.4875 (mmm) REVERT: B 911 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6802 (tm-30) REVERT: E 74 ASP cc_start: 0.7655 (m-30) cc_final: 0.7415 (m-30) REVERT: F 176 LYS cc_start: 0.8651 (ptmm) cc_final: 0.8390 (ptmt) outliers start: 51 outliers final: 26 residues processed: 321 average time/residue: 0.5931 time to fit residues: 210.4365 Evaluate side-chains 298 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 TRP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 36 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 356 ASN A 454 ASN D 79 ASN E 3 HIS ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN F 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146364 restraints weight = 23483.941| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.61 r_work: 0.3781 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 15597 Z= 0.159 Angle : 0.615 9.491 21219 Z= 0.311 Chirality : 0.045 0.262 2269 Planarity : 0.004 0.059 2726 Dihedral : 7.364 82.897 2270 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.03 % Allowed : 16.51 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 1945 helix: 1.62 (0.27), residues: 402 sheet: -0.66 (0.32), residues: 254 loop : -0.96 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 376 TYR 0.017 0.001 TYR B 580 PHE 0.029 0.002 PHE B 821 TRP 0.018 0.002 TRP B 803 HIS 0.008 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00381 (15533) covalent geometry : angle 0.60450 (21087) SS BOND : bond 0.00386 ( 54) SS BOND : angle 0.95362 ( 108) hydrogen bonds : bond 0.03887 ( 503) hydrogen bonds : angle 5.12129 ( 1461) Misc. bond : bond 0.09343 ( 2) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 3.36023 ( 6) link_NAG-ASN : bond 0.00472 ( 6) link_NAG-ASN : angle 2.81518 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.433 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 162 THR cc_start: 0.8934 (p) cc_final: 0.8693 (t) REVERT: A 175 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7536 (ttpp) REVERT: A 191 ASP cc_start: 0.7781 (m-30) cc_final: 0.7521 (m-30) REVERT: A 426 VAL cc_start: 0.8647 (t) cc_final: 0.8385 (t) REVERT: A 502 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7521 (pp) REVERT: A 659 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6586 (tmm) REVERT: A 923 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7275 (tt) REVERT: A 949 SER cc_start: 0.5030 (OUTLIER) cc_final: 0.4449 (t) REVERT: A 1007 ASP cc_start: 0.3724 (OUTLIER) cc_final: 0.2538 (p0) REVERT: B 396 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7910 (mtmt) REVERT: B 600 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6563 (t) REVERT: B 638 PHE cc_start: 0.6954 (m-80) cc_final: 0.6327 (m-80) REVERT: B 884 MET cc_start: 0.4903 (mmm) cc_final: 0.4591 (mmm) REVERT: B 911 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6535 (tm-30) REVERT: E 74 ASP cc_start: 0.7284 (m-30) cc_final: 0.7049 (m-30) REVERT: F 232 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8203 (ttpp) outliers start: 65 outliers final: 34 residues processed: 323 average time/residue: 0.5674 time to fit residues: 204.4047 Evaluate side-chains 319 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 TRP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 356 ASN A 454 ASN ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 HIS E 64 HIS F 230 ASN F 278 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.174840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144058 restraints weight = 23224.115| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.55 r_work: 0.3758 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 15597 Z= 0.250 Angle : 0.676 10.760 21219 Z= 0.342 Chirality : 0.048 0.266 2269 Planarity : 0.005 0.066 2726 Dihedral : 7.581 82.176 2268 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.03 % Allowed : 17.13 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 1945 helix: 1.34 (0.27), residues: 399 sheet: -0.81 (0.31), residues: 257 loop : -0.99 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 376 TYR 0.021 0.002 TYR B 580 PHE 0.027 0.002 PHE B 821 TRP 0.018 0.002 TRP A1006 HIS 0.015 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00599 (15533) covalent geometry : angle 0.66297 (21087) SS BOND : bond 0.00469 ( 54) SS BOND : angle 1.26522 ( 108) hydrogen bonds : bond 0.04407 ( 503) hydrogen bonds : angle 5.14821 ( 1461) Misc. bond : bond 0.12564 ( 2) link_BETA1-4 : bond 0.00703 ( 2) link_BETA1-4 : angle 3.49475 ( 6) link_NAG-ASN : bond 0.00703 ( 6) link_NAG-ASN : angle 3.06331 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 287 time to evaluate : 0.573 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: A 162 THR cc_start: 0.9019 (p) cc_final: 0.8789 (t) REVERT: A 175 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7661 (ttpp) REVERT: A 426 VAL cc_start: 0.8699 (t) cc_final: 0.8459 (t) REVERT: A 485 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7751 (pp) REVERT: A 502 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 539 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: A 659 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6637 (tmm) REVERT: A 923 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 396 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8023 (mtmt) REVERT: B 469 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.6902 (mtpt) REVERT: B 600 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6719 (t) REVERT: B 740 TRP cc_start: 0.7493 (m100) cc_final: 0.7026 (m100) REVERT: B 884 MET cc_start: 0.5212 (mmm) cc_final: 0.4826 (mmm) REVERT: B 911 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6753 (tm-30) REVERT: E 123 PHE cc_start: 0.8855 (t80) cc_final: 0.8575 (t80) REVERT: F 232 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8502 (ttpp) REVERT: F 266 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8507 (mtmm) REVERT: F 341 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7867 (mp10) outliers start: 81 outliers final: 43 residues processed: 335 average time/residue: 0.5897 time to fit residues: 219.0815 Evaluate side-chains 328 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 341 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 157 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 356 ASN A 454 ASN E 3 HIS E 98 HIS E 132 GLN F 200 ASN F 230 ASN F 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146719 restraints weight = 23281.226| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.53 r_work: 0.3766 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 15597 Z= 0.172 Angle : 0.619 10.758 21219 Z= 0.313 Chirality : 0.046 0.288 2269 Planarity : 0.005 0.061 2726 Dihedral : 7.239 87.899 2264 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.72 % Allowed : 18.31 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 1945 helix: 1.54 (0.27), residues: 399 sheet: -0.69 (0.32), residues: 246 loop : -0.95 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 376 TYR 0.015 0.001 TYR A 427 PHE 0.017 0.001 PHE B 821 TRP 0.014 0.001 TRP A1006 HIS 0.010 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00415 (15533) covalent geometry : angle 0.60757 (21087) SS BOND : bond 0.00363 ( 54) SS BOND : angle 1.11848 ( 108) hydrogen bonds : bond 0.03730 ( 503) hydrogen bonds : angle 4.93528 ( 1461) Misc. bond : bond 0.09926 ( 2) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 3.39452 ( 6) link_NAG-ASN : bond 0.00531 ( 6) link_NAG-ASN : angle 2.86460 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 285 time to evaluate : 0.598 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 162 THR cc_start: 0.8989 (p) cc_final: 0.8770 (t) REVERT: A 175 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7569 (ttpp) REVERT: A 426 VAL cc_start: 0.8713 (t) cc_final: 0.8466 (t) REVERT: A 485 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 502 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7522 (pp) REVERT: A 539 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: A 923 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7474 (tt) REVERT: B 280 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4533 (tt0) REVERT: B 396 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8031 (mtmt) REVERT: B 469 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.6940 (mtpt) REVERT: B 471 THR cc_start: 0.7611 (m) cc_final: 0.6679 (p) REVERT: B 490 ARG cc_start: 0.6951 (ptt180) cc_final: 0.6733 (pmt170) REVERT: B 740 TRP cc_start: 0.7491 (m100) cc_final: 0.6960 (m100) REVERT: B 776 GLU cc_start: 0.7965 (tp30) cc_final: 0.7760 (mm-30) REVERT: B 844 ASN cc_start: 0.7145 (t0) cc_final: 0.6877 (t0) REVERT: B 884 MET cc_start: 0.5204 (mmm) cc_final: 0.4797 (mmm) REVERT: B 911 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6728 (tm-30) REVERT: E 74 ASP cc_start: 0.7607 (m-30) cc_final: 0.7387 (m-30) REVERT: E 123 PHE cc_start: 0.8853 (t80) cc_final: 0.8615 (t80) REVERT: F 232 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8567 (ttpp) REVERT: F 266 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (mtmm) REVERT: F 341 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7876 (mp10) outliers start: 76 outliers final: 40 residues processed: 326 average time/residue: 0.5871 time to fit residues: 212.3974 Evaluate side-chains 330 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 341 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 189 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 157 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 454 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 HIS E 98 HIS E 132 GLN E 144 HIS F 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.174821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144112 restraints weight = 23107.608| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.55 r_work: 0.3759 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 15597 Z= 0.217 Angle : 0.647 9.665 21219 Z= 0.328 Chirality : 0.047 0.267 2269 Planarity : 0.005 0.065 2726 Dihedral : 7.231 85.737 2262 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.21 % Allowed : 18.00 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 1945 helix: 1.42 (0.27), residues: 398 sheet: -0.73 (0.32), residues: 246 loop : -0.99 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 376 TYR 0.018 0.002 TYR B 580 PHE 0.015 0.002 PHE B 821 TRP 0.015 0.002 TRP A 889 HIS 0.010 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00524 (15533) covalent geometry : angle 0.63514 (21087) SS BOND : bond 0.00431 ( 54) SS BOND : angle 1.18199 ( 108) hydrogen bonds : bond 0.04016 ( 503) hydrogen bonds : angle 4.94204 ( 1461) Misc. bond : bond 0.11412 ( 2) link_BETA1-4 : bond 0.00620 ( 2) link_BETA1-4 : angle 3.44929 ( 6) link_NAG-ASN : bond 0.00619 ( 6) link_NAG-ASN : angle 3.01350 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 282 time to evaluate : 0.715 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: A 162 THR cc_start: 0.9009 (p) cc_final: 0.8778 (t) REVERT: A 175 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7583 (ttpp) REVERT: A 426 VAL cc_start: 0.8699 (t) cc_final: 0.8462 (t) REVERT: A 485 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7754 (pp) REVERT: A 502 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 539 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: A 923 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 953 VAL cc_start: 0.7010 (t) cc_final: 0.6804 (m) REVERT: B 280 GLU cc_start: 0.5190 (OUTLIER) cc_final: 0.4541 (tt0) REVERT: B 396 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: B 469 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.6937 (mtpt) REVERT: B 471 THR cc_start: 0.7652 (m) cc_final: 0.6788 (p) REVERT: B 490 ARG cc_start: 0.6867 (ptt180) cc_final: 0.6649 (pmt170) REVERT: B 524 VAL cc_start: 0.6035 (OUTLIER) cc_final: 0.5793 (p) REVERT: B 740 TRP cc_start: 0.7538 (m100) cc_final: 0.7056 (m100) REVERT: B 884 MET cc_start: 0.5181 (mmm) cc_final: 0.4752 (mmm) REVERT: B 911 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6715 (tm-30) REVERT: E 74 ASP cc_start: 0.7607 (m-30) cc_final: 0.7395 (m-30) REVERT: E 123 PHE cc_start: 0.8924 (t80) cc_final: 0.8591 (t80) REVERT: F 232 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8529 (ttpp) REVERT: F 337 GLN cc_start: 0.8309 (tt0) cc_final: 0.7981 (tt0) REVERT: F 341 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7864 (mp10) outliers start: 84 outliers final: 48 residues processed: 329 average time/residue: 0.5707 time to fit residues: 208.8263 Evaluate side-chains 334 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 341 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 186 optimal weight: 0.0070 chunk 61 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 443 ASN A 532 HIS ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 HIS F 200 ASN F 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.177076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146793 restraints weight = 23030.841| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.52 r_work: 0.3778 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 15597 Z= 0.158 Angle : 0.604 9.276 21219 Z= 0.306 Chirality : 0.045 0.306 2269 Planarity : 0.004 0.058 2726 Dihedral : 7.021 84.446 2262 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.16 % Allowed : 19.86 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1945 helix: 1.61 (0.27), residues: 398 sheet: -0.65 (0.32), residues: 246 loop : -0.92 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 571 TYR 0.013 0.001 TYR A 427 PHE 0.013 0.001 PHE B 821 TRP 0.013 0.001 TRP A 455 HIS 0.011 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00384 (15533) covalent geometry : angle 0.59321 (21087) SS BOND : bond 0.00338 ( 54) SS BOND : angle 1.06000 ( 108) hydrogen bonds : bond 0.03524 ( 503) hydrogen bonds : angle 4.78936 ( 1461) Misc. bond : bond 0.09966 ( 2) link_BETA1-4 : bond 0.00515 ( 2) link_BETA1-4 : angle 3.35971 ( 6) link_NAG-ASN : bond 0.00495 ( 6) link_NAG-ASN : angle 2.80634 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 0.601 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 162 THR cc_start: 0.9001 (p) cc_final: 0.8784 (t) REVERT: A 175 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7549 (ttpp) REVERT: A 426 VAL cc_start: 0.8689 (t) cc_final: 0.8462 (t) REVERT: A 502 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7426 (pp) REVERT: A 539 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: A 923 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7427 (tt) REVERT: B 280 GLU cc_start: 0.5184 (OUTLIER) cc_final: 0.4537 (tt0) REVERT: B 396 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (mtmt) REVERT: B 469 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.6936 (mtpt) REVERT: B 471 THR cc_start: 0.7544 (m) cc_final: 0.6627 (p) REVERT: B 524 VAL cc_start: 0.5957 (OUTLIER) cc_final: 0.5712 (p) REVERT: B 546 GLN cc_start: 0.8041 (mt0) cc_final: 0.7760 (mp10) REVERT: B 740 TRP cc_start: 0.7531 (m100) cc_final: 0.6983 (m100) REVERT: B 884 MET cc_start: 0.5224 (mmm) cc_final: 0.4804 (mmm) REVERT: B 911 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6691 (tm-30) REVERT: E 74 ASP cc_start: 0.7601 (m-30) cc_final: 0.7388 (m-30) REVERT: F 208 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8535 (mt) REVERT: F 266 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8409 (mtpp) outliers start: 67 outliers final: 44 residues processed: 312 average time/residue: 0.6059 time to fit residues: 209.1482 Evaluate side-chains 322 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 307 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 136 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 185 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 213 ASN A 443 ASN A 648 HIS ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 HIS F 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.174537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143861 restraints weight = 23241.348| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.56 r_work: 0.3756 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 15597 Z= 0.222 Angle : 0.650 10.323 21219 Z= 0.329 Chirality : 0.047 0.266 2269 Planarity : 0.005 0.064 2726 Dihedral : 7.159 83.929 2262 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.16 % Allowed : 20.30 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 1945 helix: 1.42 (0.27), residues: 398 sheet: -0.70 (0.32), residues: 246 loop : -0.96 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 376 TYR 0.017 0.002 TYR B 580 PHE 0.014 0.002 PHE B 821 TRP 0.015 0.002 TRP B 910 HIS 0.010 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00534 (15533) covalent geometry : angle 0.63725 (21087) SS BOND : bond 0.00440 ( 54) SS BOND : angle 1.21329 ( 108) hydrogen bonds : bond 0.03958 ( 503) hydrogen bonds : angle 4.86750 ( 1461) Misc. bond : bond 0.12326 ( 2) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 3.41217 ( 6) link_NAG-ASN : bond 0.00623 ( 6) link_NAG-ASN : angle 3.03141 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 0.468 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 162 THR cc_start: 0.9013 (p) cc_final: 0.8773 (t) REVERT: A 175 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7568 (ttpp) REVERT: A 426 VAL cc_start: 0.8682 (t) cc_final: 0.8459 (t) REVERT: A 485 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 502 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 539 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: A 874 LYS cc_start: 0.6984 (mmpt) cc_final: 0.6618 (mmpt) REVERT: A 953 VAL cc_start: 0.6989 (t) cc_final: 0.6772 (m) REVERT: B 280 GLU cc_start: 0.5189 (OUTLIER) cc_final: 0.4535 (tt0) REVERT: B 396 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: B 469 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.6964 (mtpt) REVERT: B 524 VAL cc_start: 0.5937 (OUTLIER) cc_final: 0.5690 (p) REVERT: B 740 TRP cc_start: 0.7562 (m100) cc_final: 0.7096 (m100) REVERT: B 884 MET cc_start: 0.5288 (mmm) cc_final: 0.4837 (mmm) REVERT: F 89 VAL cc_start: 0.8654 (p) cc_final: 0.8386 (m) REVERT: F 173 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7340 (mm-30) outliers start: 67 outliers final: 52 residues processed: 316 average time/residue: 0.5914 time to fit residues: 206.5927 Evaluate side-chains 334 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 307 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 49 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 356 ASN A 443 ASN B 651 HIS ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 HIS F 200 ASN F 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.177030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146626 restraints weight = 23197.147| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.55 r_work: 0.3797 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 15597 Z= 0.122 Angle : 0.580 8.827 21219 Z= 0.294 Chirality : 0.044 0.262 2269 Planarity : 0.004 0.055 2726 Dihedral : 6.808 82.908 2262 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.85 % Allowed : 20.79 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1945 helix: 1.75 (0.27), residues: 402 sheet: -0.61 (0.32), residues: 260 loop : -0.85 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 376 TYR 0.013 0.001 TYR B 580 PHE 0.011 0.001 PHE B 821 TRP 0.011 0.001 TRP A 455 HIS 0.009 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00296 (15533) covalent geometry : angle 0.57096 (21087) SS BOND : bond 0.00266 ( 54) SS BOND : angle 0.90087 ( 108) hydrogen bonds : bond 0.03142 ( 503) hydrogen bonds : angle 4.63520 ( 1461) Misc. bond : bond 0.09489 ( 2) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 3.26086 ( 6) link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 2.60819 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 0.608 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 162 THR cc_start: 0.9003 (p) cc_final: 0.8780 (t) REVERT: A 175 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7526 (ttpp) REVERT: A 426 VAL cc_start: 0.8686 (t) cc_final: 0.8475 (t) REVERT: A 502 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7474 (pp) REVERT: A 949 SER cc_start: 0.4913 (OUTLIER) cc_final: 0.4457 (t) REVERT: A 953 VAL cc_start: 0.6942 (t) cc_final: 0.6718 (m) REVERT: B 280 GLU cc_start: 0.5163 (OUTLIER) cc_final: 0.4516 (tt0) REVERT: B 396 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7956 (mtmt) REVERT: B 469 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: B 524 VAL cc_start: 0.5782 (OUTLIER) cc_final: 0.5485 (p) REVERT: B 599 LYS cc_start: 0.7928 (pttm) cc_final: 0.7432 (pttm) REVERT: B 637 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7648 (tmm-80) REVERT: B 720 ARG cc_start: 0.8259 (ptt90) cc_final: 0.8035 (ptt90) REVERT: B 740 TRP cc_start: 0.7522 (m100) cc_final: 0.7069 (m100) REVERT: B 781 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.6815 (pp) REVERT: B 884 MET cc_start: 0.5241 (mmm) cc_final: 0.4814 (mmm) REVERT: E 74 ASP cc_start: 0.7568 (m-30) cc_final: 0.7334 (m-30) REVERT: F 173 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7279 (mm-30) outliers start: 62 outliers final: 38 residues processed: 312 average time/residue: 0.5973 time to fit residues: 206.6681 Evaluate side-chains 314 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 103 optimal weight: 0.0050 chunk 6 optimal weight: 0.0970 chunk 167 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 213 ASN A 356 ASN A 443 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN E 3 HIS F 144 ASN F 230 ASN F 249 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.175924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.145127 restraints weight = 23306.634| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.57 r_work: 0.3764 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 15597 Z= 0.183 Angle : 0.624 10.042 21219 Z= 0.316 Chirality : 0.046 0.258 2269 Planarity : 0.005 0.061 2726 Dihedral : 6.900 82.991 2260 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.35 % Allowed : 21.73 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1945 helix: 1.63 (0.27), residues: 398 sheet: -0.62 (0.32), residues: 246 loop : -0.87 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 374 TYR 0.019 0.002 TYR B 580 PHE 0.012 0.001 PHE F 280 TRP 0.022 0.001 TRP B 910 HIS 0.018 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00442 (15533) covalent geometry : angle 0.61294 (21087) SS BOND : bond 0.00374 ( 54) SS BOND : angle 1.08070 ( 108) hydrogen bonds : bond 0.03658 ( 503) hydrogen bonds : angle 4.74362 ( 1461) Misc. bond : bond 0.11389 ( 2) link_BETA1-4 : bond 0.00729 ( 2) link_BETA1-4 : angle 3.26006 ( 6) link_NAG-ASN : bond 0.00524 ( 6) link_NAG-ASN : angle 2.84942 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.559 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: A 162 THR cc_start: 0.9018 (p) cc_final: 0.8787 (t) REVERT: A 175 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7574 (ttpp) REVERT: A 426 VAL cc_start: 0.8688 (t) cc_final: 0.8470 (t) REVERT: A 502 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7472 (pp) REVERT: A 953 VAL cc_start: 0.6984 (t) cc_final: 0.6759 (m) REVERT: B 280 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4529 (tt0) REVERT: B 396 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8045 (mtmt) REVERT: B 469 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.6951 (mtpt) REVERT: B 524 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5550 (p) REVERT: B 546 GLN cc_start: 0.8098 (mt0) cc_final: 0.7803 (mp10) REVERT: B 599 LYS cc_start: 0.7982 (pttm) cc_final: 0.7407 (pttm) REVERT: B 649 MET cc_start: 0.6437 (mtm) cc_final: 0.5954 (mtm) REVERT: B 740 TRP cc_start: 0.7554 (m100) cc_final: 0.7073 (m100) REVERT: B 781 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.6892 (pp) REVERT: B 884 MET cc_start: 0.5369 (mmm) cc_final: 0.4932 (mmm) REVERT: F 89 VAL cc_start: 0.8629 (p) cc_final: 0.8356 (m) REVERT: F 173 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7386 (mm-30) outliers start: 54 outliers final: 40 residues processed: 302 average time/residue: 0.5901 time to fit residues: 197.6205 Evaluate side-chains 313 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 201 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 62 optimal weight: 0.0070 chunk 164 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 356 ASN A 443 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN E 3 HIS F 144 ASN F 200 ASN F 230 ASN F 249 GLN F 337 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.175805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145525 restraints weight = 23128.770| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.49 r_work: 0.3776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15597 Z= 0.146 Angle : 0.606 9.397 21219 Z= 0.308 Chirality : 0.045 0.257 2269 Planarity : 0.005 0.056 2726 Dihedral : 6.820 82.635 2260 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.29 % Allowed : 21.91 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1945 helix: 1.70 (0.27), residues: 399 sheet: -0.58 (0.32), residues: 256 loop : -0.82 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 374 TYR 0.017 0.001 TYR B 580 PHE 0.010 0.001 PHE B 821 TRP 0.018 0.001 TRP B 910 HIS 0.017 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00355 (15533) covalent geometry : angle 0.59641 (21087) SS BOND : bond 0.00317 ( 54) SS BOND : angle 0.97860 ( 108) hydrogen bonds : bond 0.03384 ( 503) hydrogen bonds : angle 4.68773 ( 1461) Misc. bond : bond 0.10488 ( 2) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 3.24441 ( 6) link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 2.70010 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6751.81 seconds wall clock time: 115 minutes 49.40 seconds (6949.40 seconds total)