Starting phenix.real_space_refine on Fri Jul 3 17:25:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hej_52078/07_2026/9hej_52078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hej_52078/07_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_52078/07_2026/9hej_52078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hej_52078/07_2026/9hej_52078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hej_52078/07_2026/9hej_52078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hej_52078/07_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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 6 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, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.15, per 1000 atoms: 0.21 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: 1.27 Conformation dependent library (CDL) restraints added in 660.8 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: 0.50 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: 2.65 Time building geometry restraints manager: 1.63 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 3.250 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 3.250 ... (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: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.070 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: 0.010 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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/Z covalent geometry : bond 0.00397 / 0.17 (15533) covalent geometry : angle 0.72854 / 0.38 (21087) SS BOND : bond 0.00323 / 0.18 ( 54) SS BOND : angle 2.12401 / 1.38 ( 108) hydrogen bonds : bond 0.21679 / 14.70 ( 503) hydrogen bonds : angle 7.82237 / 5.46 ( 1461) Misc. bond : bond 0.09752 / 4.65 ( 2) link_BETA1-4 : bond 0.00675 / 0.35 ( 2) link_BETA1-4 : angle 2.69551 / 1.20 ( 6) link_NAG-ASN : bond 0.00312 / 0.16 ( 6) link_NAG-ASN : angle 2.31012 / 1.53 ( 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 : 0.433 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: 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: 0.5421 time to fit residues: 182.6032 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 : 0.537 ------------------------------------------------------------------------------- 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... ** 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 = 0.4290 r_free = 0.4290 target = 0.177387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145844 restraints weight = 23268.227| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.60 r_work: 0.3790 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0937 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= 0.166 Angle : 0.656 9.576 21219 Z= 0.333 Chirality : 0.046 0.271 2269 Planarity : 0.005 0.061 2726 Dihedral : 7.921 84.484 2300 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.54 % Allowed : 16.20 % Favored : 80.26 % 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: -0.61 (0.18), residues: 1945 helix: 1.55 (0.27), residues: 402 sheet: -0.72 (0.31), residues: 266 loop : -1.02 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 376 TYR 0.019 0.001 TYR B 580 PHE 0.018 0.002 PHE A 650 TRP 0.022 0.002 TRP A 612 HIS 0.008 0.001 HIS B 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (15533) covalent geometry : angle 0.64631 / 0.33 (21087) SS BOND : bond 0.00355 / 0.19 ( 54) SS BOND : angle 1.06833 / 0.68 ( 108) hydrogen bonds : bond 0.04194 / 2.86 ( 503) hydrogen bonds : angle 5.46905 / 3.85 ( 1461) Misc. bond : bond 0.09750 / 4.76 ( 2) link_BETA1-4 : bond 0.00597 / 0.31 ( 2) link_BETA1-4 : angle 3.45526 / 1.58 ( 6) link_NAG-ASN : bond 0.00448 / 0.23 ( 6) link_NAG-ASN : angle 2.79681 / 1.84 ( 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 350 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 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: A 162 THR cc_start: 0.9063 (p) cc_final: 0.8800 (t) REVERT: A 175 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7829 (ttpp) REVERT: A 191 ASP cc_start: 0.8113 (m-30) cc_final: 0.7815 (m-30) REVERT: A 426 VAL cc_start: 0.8793 (t) cc_final: 0.8548 (t) REVERT: B 599 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7570 (pttm) REVERT: B 600 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6731 (t) REVERT: B 638 PHE cc_start: 0.7257 (m-80) cc_final: 0.6607 (m-80) REVERT: B 776 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: B 884 MET cc_start: 0.5111 (mmm) cc_final: 0.4895 (mmm) REVERT: B 911 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6709 (tm-30) REVERT: E 74 ASP cc_start: 0.7670 (m-30) cc_final: 0.7433 (m-30) REVERT: F 176 LYS cc_start: 0.8658 (ptmm) cc_final: 0.8399 (ptmt) outliers start: 57 outliers final: 28 residues processed: 324 average time/residue: 0.5610 time to fit residues: 201.8951 Evaluate side-chains 305 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 365 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 515 LEU Chi-restraints excluded: chain B residue 599 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 B residue 776 GLU 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: 0.3980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 186 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 454 ASN D 79 ASN E 3 HIS E 64 HIS E 132 GLN F 200 ASN F 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.178065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147147 restraints weight = 23545.089| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.62 r_work: 0.3792 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 15597 Z= 0.140 Angle : 0.601 9.077 21219 Z= 0.305 Chirality : 0.044 0.261 2269 Planarity : 0.004 0.056 2726 Dihedral : 7.278 82.945 2272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.91 % Allowed : 16.88 % Favored : 79.21 % 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: -0.47 (0.18), residues: 1945 helix: 1.71 (0.27), residues: 402 sheet: -0.66 (0.31), residues: 254 loop : -0.93 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 376 TYR 0.016 0.001 TYR B 580 PHE 0.030 0.001 PHE B 821 TRP 0.016 0.001 TRP A1006 HIS 0.009 0.001 HIS B 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15533) covalent geometry : angle 0.59114 / 0.30 (21087) SS BOND : bond 0.00313 / 0.17 ( 54) SS BOND : angle 0.90728 / 0.56 ( 108) hydrogen bonds : bond 0.03730 / 2.54 ( 503) hydrogen bonds : angle 5.09343 / 3.59 ( 1461) Misc. bond : bond 0.08737 / 4.24 ( 2) link_BETA1-4 : bond 0.00267 / 0.14 ( 2) link_BETA1-4 : angle 3.28127 / 1.52 ( 6) link_NAG-ASN : bond 0.00435 / 0.22 ( 6) link_NAG-ASN : angle 2.75214 / 1.80 ( 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 354 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 0.710 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: 0.9027 (p) cc_final: 0.8805 (t) REVERT: A 175 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7635 (ttpp) REVERT: A 191 ASP cc_start: 0.8091 (m-30) cc_final: 0.7781 (m-30) REVERT: A 426 VAL cc_start: 0.8752 (t) cc_final: 0.8506 (t) REVERT: A 502 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7617 (pp) REVERT: A 659 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6681 (tmm) REVERT: A 923 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7369 (tt) REVERT: A 926 ASP cc_start: 0.5261 (OUTLIER) cc_final: 0.5051 (t0) REVERT: A 1007 ASP cc_start: 0.3859 (OUTLIER) cc_final: 0.2695 (p0) REVERT: B 396 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: B 600 THR cc_start: 0.7092 (OUTLIER) cc_final: 0.6787 (t) REVERT: B 638 PHE cc_start: 0.7208 (m-80) cc_final: 0.6575 (m-80) REVERT: B 776 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: B 884 MET cc_start: 0.5110 (mmm) cc_final: 0.4779 (mmm) REVERT: B 911 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6885 (tm-30) REVERT: E 74 ASP cc_start: 0.7648 (m-30) cc_final: 0.7419 (m-30) REVERT: F 120 MET cc_start: 0.8702 (ptp) cc_final: 0.8489 (ptm) REVERT: F 232 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8436 (ttpp) outliers start: 63 outliers final: 29 residues processed: 327 average time/residue: 0.5457 time to fit residues: 199.3326 Evaluate side-chains 316 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 855 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 VAL 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 748 TRP Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 776 GLU 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 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: 2.9990 chunk 37 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 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... ** 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** D 79 ASN E 3 HIS E 132 GLN F 230 ASN F 278 HIS F 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146012 restraints weight = 23194.078| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.60 r_work: 0.3744 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 15597 Z= 0.247 Angle : 0.677 10.687 21219 Z= 0.343 Chirality : 0.048 0.262 2269 Planarity : 0.005 0.064 2726 Dihedral : 7.526 89.560 2266 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.90 % Allowed : 17.13 % Favored : 77.96 % 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: -0.63 (0.18), residues: 1945 helix: 1.40 (0.27), residues: 399 sheet: -0.69 (0.31), residues: 260 loop : -0.99 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 376 TYR 0.020 0.002 TYR B 580 PHE 0.028 0.002 PHE B 821 TRP 0.014 0.002 TRP B 910 HIS 0.016 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (15533) covalent geometry : angle 0.66384 / 0.34 (21087) SS BOND : bond 0.00472 / 0.25 ( 54) SS BOND : angle 1.28787 / 0.88 ( 108) hydrogen bonds : bond 0.04414 / 3.06 ( 503) hydrogen bonds : angle 5.13697 / 3.62 ( 1461) Misc. bond : bond 0.12335 / 6.22 ( 2) link_BETA1-4 : bond 0.00798 / 0.42 ( 2) link_BETA1-4 : angle 3.55268 / 1.56 ( 6) link_NAG-ASN : bond 0.00687 / 0.35 ( 6) link_NAG-ASN : angle 3.03785 / 2.01 ( 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 370 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 291 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 THR cc_start: 0.9023 (p) cc_final: 0.8801 (t) REVERT: A 175 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7681 (ttpp) REVERT: A 336 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7579 (mp-120) REVERT: A 426 VAL cc_start: 0.8701 (t) cc_final: 0.8467 (t) REVERT: A 485 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7739 (pp) REVERT: A 502 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 539 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: A 659 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6658 (tmm) REVERT: A 923 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 926 ASP cc_start: 0.5727 (OUTLIER) cc_final: 0.5275 (t0) REVERT: B 396 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8029 (mtmt) REVERT: B 469 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.6925 (mtpt) REVERT: B 600 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6775 (t) REVERT: B 740 TRP cc_start: 0.7490 (m100) cc_final: 0.7282 (m100) REVERT: B 776 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: B 884 MET cc_start: 0.5223 (mmm) cc_final: 0.4843 (mmm) REVERT: B 911 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6818 (tm-30) REVERT: E 123 PHE cc_start: 0.8851 (t80) cc_final: 0.8566 (t80) REVERT: F 232 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8476 (ttpp) REVERT: F 266 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8512 (mtmm) REVERT: F 341 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7868 (mp10) outliers start: 79 outliers final: 42 residues processed: 334 average time/residue: 0.5857 time to fit residues: 216.9272 Evaluate side-chains 328 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 336 GLN 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 855 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ASP 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 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 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 776 GLU 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 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: 0.6980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 116 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 130 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 144 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 356 ASN A 454 ASN D 79 ASN E 3 HIS E 98 HIS F 200 ASN F 230 ASN F 278 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.177202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146559 restraints weight = 23454.024| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.56 r_work: 0.3786 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 15597 Z= 0.146 Angle : 0.597 10.426 21219 Z= 0.301 Chirality : 0.044 0.286 2269 Planarity : 0.004 0.056 2726 Dihedral : 7.028 86.387 2264 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.28 % Allowed : 18.50 % Favored : 77.22 % 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: -0.42 (0.19), residues: 1945 helix: 1.70 (0.27), residues: 399 sheet: -0.69 (0.31), residues: 266 loop : -0.86 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 571 TYR 0.014 0.001 TYR B 580 PHE 0.015 0.001 PHE B 821 TRP 0.011 0.001 TRP A 455 HIS 0.011 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (15533) covalent geometry : angle 0.58609 / 0.30 (21087) SS BOND : bond 0.00317 / 0.17 ( 54) SS BOND : angle 1.04212 / 0.73 ( 108) hydrogen bonds : bond 0.03485 / 2.40 ( 503) hydrogen bonds : angle 4.85019 / 3.40 ( 1461) Misc. bond : bond 0.09062 / 4.51 ( 2) link_BETA1-4 : bond 0.00431 / 0.22 ( 2) link_BETA1-4 : angle 3.28425 / 1.56 ( 6) link_NAG-ASN : bond 0.00497 / 0.26 ( 6) link_NAG-ASN : angle 2.75200 / 1.83 ( 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 356 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 287 time to evaluate : 0.624 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: 0.8991 (p) cc_final: 0.8785 (t) REVERT: A 175 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7563 (ttpp) REVERT: A 426 VAL cc_start: 0.8703 (t) cc_final: 0.8462 (t) REVERT: A 502 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7494 (pp) REVERT: A 539 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: A 923 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7476 (tt) REVERT: A 926 ASP cc_start: 0.5391 (OUTLIER) cc_final: 0.5069 (t0) REVERT: B 280 GLU cc_start: 0.5149 (OUTLIER) cc_final: 0.4505 (tt0) REVERT: B 396 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: B 469 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.6963 (mtpt) REVERT: B 471 THR cc_start: 0.7567 (m) cc_final: 0.6613 (p) REVERT: B 599 LYS cc_start: 0.7971 (pttm) cc_final: 0.7532 (pttm) REVERT: B 740 TRP cc_start: 0.7468 (m100) cc_final: 0.7014 (m100) REVERT: B 776 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: B 884 MET cc_start: 0.5165 (mmm) cc_final: 0.4762 (mmm) REVERT: B 911 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6773 (tm-30) REVERT: E 74 ASP cc_start: 0.7649 (m-30) cc_final: 0.7429 (m-30) REVERT: E 123 PHE cc_start: 0.8820 (t80) cc_final: 0.8581 (t80) REVERT: F 120 MET cc_start: 0.8703 (ptp) cc_final: 0.8500 (ptm) REVERT: F 232 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8555 (ttpp) REVERT: F 266 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (mtmm) REVERT: F 341 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7858 (mp10) outliers start: 69 outliers final: 36 residues processed: 323 average time/residue: 0.5678 time to fit residues: 204.0398 Evaluate side-chains 321 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 345 CYS 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 391 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 GLU 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 926 ASP 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 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 754 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 776 GLU 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 133 ILE Chi-restraints excluded: chain F residue 188 ILE 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: 0.9990 chunk 66 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 454 ASN E 3 HIS E 98 HIS E 144 HIS F 230 ASN F 278 HIS F 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145074 restraints weight = 23088.852| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.54 r_work: 0.3751 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 15597 Z= 0.241 Angle : 0.666 10.088 21219 Z= 0.337 Chirality : 0.048 0.265 2269 Planarity : 0.005 0.064 2726 Dihedral : 7.125 85.323 2258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.90 % Allowed : 18.19 % Favored : 76.91 % 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: 1.42 (0.27), residues: 398 sheet: -0.73 (0.32), residues: 246 loop : -0.97 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 376 TYR 0.019 0.002 TYR B 580 PHE 0.016 0.002 PHE B 821 TRP 0.013 0.002 TRP A 455 HIS 0.011 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (15533) covalent geometry : angle 0.65315 / 0.33 (21087) SS BOND : bond 0.00472 / 0.25 ( 54) SS BOND : angle 1.25398 / 0.87 ( 108) hydrogen bonds : bond 0.04192 / 2.88 ( 503) hydrogen bonds : angle 4.95897 / 3.49 ( 1461) Misc. bond : bond 0.12128 / 6.21 ( 2) link_BETA1-4 : bond 0.00701 / 0.37 ( 2) link_BETA1-4 : angle 3.48070 / 1.53 ( 6) link_NAG-ASN : bond 0.00652 / 0.34 ( 6) link_NAG-ASN : angle 3.09844 / 2.05 ( 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 351 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 272 time to evaluate : 0.703 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: 0.9040 (p) cc_final: 0.8804 (t) REVERT: A 175 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7583 (ttpp) REVERT: A 426 VAL cc_start: 0.8692 (t) cc_final: 0.8455 (t) REVERT: A 485 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 502 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7519 (pp) REVERT: A 539 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: A 926 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5166 (t0) REVERT: A 953 VAL cc_start: 0.7033 (t) cc_final: 0.6806 (m) REVERT: B 280 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4548 (tt0) REVERT: B 396 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8033 (mtmt) REVERT: B 469 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.6947 (mtpt) REVERT: B 471 THR cc_start: 0.7672 (m) cc_final: 0.7213 (m) REVERT: B 600 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6704 (t) REVERT: B 740 TRP cc_start: 0.7528 (m100) cc_final: 0.7041 (m100) REVERT: B 776 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: B 781 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.6956 (pp) REVERT: B 884 MET cc_start: 0.5351 (mmm) cc_final: 0.4907 (mmm) REVERT: E 74 ASP cc_start: 0.7604 (m-30) cc_final: 0.7389 (m-30) REVERT: F 232 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8578 (ttpp) REVERT: F 341 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7859 (mp10) outliers start: 79 outliers final: 42 residues processed: 319 average time/residue: 0.5385 time to fit residues: 191.3529 Evaluate side-chains 323 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 391 GLN 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 926 ASP 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 600 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 811 LYS 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 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 188 ILE Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 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: 0.8980 chunk 70 optimal weight: 0.9980 chunk 186 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 105 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 356 ASN A 443 ASN A 532 HIS E 3 HIS F 200 ASN F 230 ASN F 278 HIS 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 = 0.176758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146463 restraints weight = 23084.186| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.53 r_work: 0.3776 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 15597 Z= 0.172 Angle : 0.616 9.438 21219 Z= 0.312 Chirality : 0.045 0.267 2269 Planarity : 0.004 0.061 2726 Dihedral : 6.935 84.148 2258 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.78 % Allowed : 18.93 % Favored : 76.29 % 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: -0.51 (0.19), residues: 1945 helix: 1.60 (0.27), residues: 398 sheet: -0.68 (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 B 490 TYR 0.016 0.001 TYR A 427 PHE 0.014 0.001 PHE B 821 TRP 0.016 0.001 TRP A 889 HIS 0.010 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (15533) covalent geometry : angle 0.60426 / 0.31 (21087) SS BOND : bond 0.00358 / 0.19 ( 54) SS BOND : angle 1.12008 / 0.77 ( 108) hydrogen bonds : bond 0.03651 / 2.52 ( 503) hydrogen bonds : angle 4.82654 / 3.39 ( 1461) Misc. bond : bond 0.10410 / 5.25 ( 2) link_BETA1-4 : bond 0.00511 / 0.27 ( 2) link_BETA1-4 : angle 3.37710 / 1.57 ( 6) link_NAG-ASN : bond 0.00542 / 0.28 ( 6) link_NAG-ASN : angle 2.89517 / 1.92 ( 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 349 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 272 time to evaluate : 0.510 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: 0.9009 (p) cc_final: 0.8785 (t) REVERT: A 175 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7572 (ttpp) REVERT: A 391 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 426 VAL cc_start: 0.8677 (t) cc_final: 0.8447 (t) REVERT: A 485 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7737 (pp) REVERT: A 502 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (pp) REVERT: A 539 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: A 659 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6599 (tmm) REVERT: A 923 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 926 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.5005 (t0) REVERT: B 280 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4544 (tt0) REVERT: B 396 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: B 469 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.6934 (mtpt) REVERT: B 471 THR cc_start: 0.7590 (m) cc_final: 0.6653 (p) REVERT: B 481 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6813 (p) REVERT: B 524 VAL cc_start: 0.5996 (OUTLIER) cc_final: 0.5782 (p) REVERT: B 546 GLN cc_start: 0.8064 (mt0) cc_final: 0.7779 (mp10) REVERT: B 599 LYS cc_start: 0.8015 (pttm) cc_final: 0.7558 (pttm) REVERT: B 600 THR cc_start: 0.7043 (OUTLIER) cc_final: 0.6759 (t) REVERT: B 740 TRP cc_start: 0.7518 (m100) cc_final: 0.7020 (m100) REVERT: B 884 MET cc_start: 0.5354 (mmm) cc_final: 0.4904 (mmm) REVERT: E 74 ASP cc_start: 0.7595 (m-30) cc_final: 0.7386 (m-30) REVERT: E 123 PHE cc_start: 0.8852 (t80) cc_final: 0.8551 (t80) REVERT: F 120 MET cc_start: 0.8750 (ptp) cc_final: 0.8535 (ptm) REVERT: F 232 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8468 (ttpp) REVERT: F 266 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8409 (mtpp) REVERT: F 341 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7861 (mp10) outliers start: 77 outliers final: 42 residues processed: 319 average time/residue: 0.5526 time to fit residues: 196.4897 Evaluate side-chains 324 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 391 GLN 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 659 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ASP 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 481 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 767 ASN 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 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 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 188 ILE Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 341 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 136 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.0270 chunk 193 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 188 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 213 ASN A 356 ASN A 443 ASN B 894 GLN E 3 HIS F 230 ASN F 278 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.176495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145945 restraints weight = 23353.399| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.56 r_work: 0.3769 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 15597 Z= 0.149 Angle : 0.605 9.031 21219 Z= 0.307 Chirality : 0.045 0.339 2269 Planarity : 0.005 0.065 2726 Dihedral : 6.837 83.645 2258 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.10 % Allowed : 20.48 % Favored : 75.42 % 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: -0.45 (0.19), residues: 1945 helix: 1.69 (0.27), residues: 398 sheet: -0.66 (0.32), residues: 246 loop : -0.90 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 490 TYR 0.012 0.001 TYR A 427 PHE 0.011 0.001 PHE B 821 TRP 0.012 0.001 TRP B 910 HIS 0.010 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15533) covalent geometry : angle 0.59421 / 0.30 (21087) SS BOND : bond 0.00336 / 0.18 ( 54) SS BOND : angle 1.02345 / 0.71 ( 108) hydrogen bonds : bond 0.03495 / 2.41 ( 503) hydrogen bonds : angle 4.74145 / 3.33 ( 1461) Misc. bond : bond 0.09709 / 4.82 ( 2) link_BETA1-4 : bond 0.00479 / 0.25 ( 2) link_BETA1-4 : angle 3.34727 / 1.56 ( 6) link_NAG-ASN : bond 0.00484 / 0.25 ( 6) link_NAG-ASN : angle 2.79772 / 1.86 ( 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 342 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 0.489 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: symmetry clash REVERT: A 162 THR cc_start: 0.9020 (p) cc_final: 0.8793 (t) REVERT: A 175 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7540 (ttpp) REVERT: A 426 VAL cc_start: 0.8692 (t) cc_final: 0.8464 (t) REVERT: A 502 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7486 (pp) REVERT: A 539 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 923 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 926 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.4955 (t0) REVERT: A 953 VAL cc_start: 0.6989 (t) cc_final: 0.6774 (m) REVERT: A 970 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.4090 (mp) REVERT: B 280 GLU cc_start: 0.5187 (OUTLIER) cc_final: 0.4540 (tt0) REVERT: B 372 GLU cc_start: 0.7651 (pm20) cc_final: 0.7432 (pm20) REVERT: B 396 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8019 (mtmt) REVERT: B 469 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.6924 (mtpt) REVERT: B 471 THR cc_start: 0.7526 (m) cc_final: 0.6571 (p) REVERT: B 524 VAL cc_start: 0.5901 (OUTLIER) cc_final: 0.5699 (p) REVERT: B 600 THR cc_start: 0.7029 (OUTLIER) cc_final: 0.6747 (t) REVERT: B 740 TRP cc_start: 0.7506 (m100) cc_final: 0.7011 (m100) REVERT: B 884 MET cc_start: 0.5358 (mmm) cc_final: 0.4894 (mmm) REVERT: E 74 ASP cc_start: 0.7591 (m-30) cc_final: 0.7379 (m-30) REVERT: E 123 PHE cc_start: 0.8876 (t80) cc_final: 0.8541 (t80) REVERT: F 120 MET cc_start: 0.8745 (ptp) cc_final: 0.8523 (ptm) REVERT: F 266 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8412 (mtpp) REVERT: F 337 GLN cc_start: 0.8248 (tt0) cc_final: 0.7913 (mt0) REVERT: F 341 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7872 (mp10) outliers start: 66 outliers final: 41 residues processed: 314 average time/residue: 0.5573 time to fit residues: 194.5678 Evaluate side-chains 323 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 477 GLU Chi-restraints excluded: chain A residue 501 SER 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 926 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 970 LEU 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 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 548 GLU 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 767 ASN Chi-restraints excluded: chain D residue 17 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 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 95 ASN 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 215 GLU Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 341 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 49 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 151 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 140 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 155 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 overall best weight: 0.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 356 ASN A 443 ASN A 648 HIS B 657 GLN E 3 HIS F 144 ASN F 200 ASN F 230 ASN F 278 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.179916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149532 restraints weight = 23345.877| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.56 r_work: 0.3818 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.002 0.107 15597 Z= 0.099 Angle : 0.561 7.728 21219 Z= 0.285 Chirality : 0.043 0.290 2269 Planarity : 0.004 0.054 2726 Dihedral : 6.447 82.575 2258 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.35 % Allowed : 21.54 % Favored : 75.11 % 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: -0.23 (0.19), residues: 1945 helix: 1.99 (0.28), residues: 402 sheet: -0.65 (0.32), residues: 256 loop : -0.77 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 490 TYR 0.008 0.001 TYR A 427 PHE 0.010 0.001 PHE B 821 TRP 0.012 0.001 TRP A 958 HIS 0.012 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15533) covalent geometry : angle 0.55253 / 0.28 (21087) SS BOND : bond 0.00238 / 0.14 ( 54) SS BOND : angle 0.80064 / 0.55 ( 108) hydrogen bonds : bond 0.02861 / 1.96 ( 503) hydrogen bonds : angle 4.52781 / 3.18 ( 1461) Misc. bond : bond 0.07900 / 3.79 ( 2) link_BETA1-4 : bond 0.00456 / 0.24 ( 2) link_BETA1-4 : angle 3.19952 / 1.60 ( 6) link_NAG-ASN : bond 0.00333 / 0.17 ( 6) link_NAG-ASN : angle 2.43120 / 1.63 ( 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 331 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 0.550 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: 0.9014 (p) cc_final: 0.8788 (t) REVERT: A 175 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7488 (ttpp) REVERT: A 426 VAL cc_start: 0.8685 (t) cc_final: 0.8463 (t) REVERT: A 502 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 539 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: A 953 VAL cc_start: 0.6973 (t) cc_final: 0.6745 (m) REVERT: A 970 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.3832 (mp) REVERT: B 280 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.4540 (tt0) REVERT: B 469 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.6995 (mtpt) REVERT: B 524 VAL cc_start: 0.5748 (OUTLIER) cc_final: 0.5521 (p) REVERT: B 599 LYS cc_start: 0.7899 (pttm) cc_final: 0.7278 (pttm) REVERT: B 600 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6736 (t) REVERT: B 740 TRP cc_start: 0.7455 (m100) cc_final: 0.7029 (m100) REVERT: B 884 MET cc_start: 0.5316 (mmm) cc_final: 0.4867 (mmm) REVERT: D 138 THR cc_start: 0.8766 (p) cc_final: 0.8444 (p) REVERT: E 74 ASP cc_start: 0.7532 (m-30) cc_final: 0.7297 (m-30) REVERT: E 123 PHE cc_start: 0.8792 (t80) cc_final: 0.8475 (t80) outliers start: 54 outliers final: 30 residues processed: 306 average time/residue: 0.5498 time to fit residues: 187.3951 Evaluate side-chains 304 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 502 ILE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 970 LEU 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 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 736 HIS Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 95 ASN 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 215 GLU 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: 0.1980 chunk 6 optimal weight: 0.0000 chunk 167 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 213 ASN A 356 ASN A 443 ASN E 3 HIS F 144 ASN F 230 ASN F 249 GLN F 278 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146874 restraints weight = 23368.307| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.58 r_work: 0.3771 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2331 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= 0.168 Angle : 0.608 9.756 21219 Z= 0.308 Chirality : 0.046 0.281 2269 Planarity : 0.005 0.057 2726 Dihedral : 6.680 82.937 2258 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.36 % Allowed : 22.66 % Favored : 74.98 % 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: -0.35 (0.19), residues: 1945 helix: 1.80 (0.27), residues: 399 sheet: -0.74 (0.32), residues: 255 loop : -0.81 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 374 TYR 0.015 0.001 TYR B 580 PHE 0.011 0.001 PHE F 280 TRP 0.022 0.001 TRP B 910 HIS 0.011 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (15533) covalent geometry : angle 0.59793 / 0.30 (21087) SS BOND : bond 0.00349 / 0.18 ( 54) SS BOND : angle 1.04045 / 0.72 ( 108) hydrogen bonds : bond 0.03516 / 2.42 ( 503) hydrogen bonds : angle 4.63880 / 3.25 ( 1461) Misc. bond : bond 0.10442 / 5.17 ( 2) link_BETA1-4 : bond 0.00606 / 0.31 ( 2) link_BETA1-4 : angle 3.08518 / 1.37 ( 6) link_NAG-ASN : bond 0.00462 / 0.24 ( 6) link_NAG-ASN : angle 2.70006 / 1.80 ( 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 313 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 0.431 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 158 GLU cc_start: 0.7666 (pt0) cc_final: 0.7380 (pt0) REVERT: A 162 THR cc_start: 0.9027 (p) cc_final: 0.8797 (t) REVERT: A 175 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7550 (ttpp) REVERT: A 426 VAL cc_start: 0.8696 (t) cc_final: 0.8483 (t) REVERT: A 502 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7452 (pp) REVERT: A 539 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: A 953 VAL cc_start: 0.6984 (t) cc_final: 0.6759 (m) REVERT: B 280 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4503 (tt0) REVERT: B 469 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.6967 (mtpt) REVERT: B 524 VAL cc_start: 0.5938 (OUTLIER) cc_final: 0.5713 (p) REVERT: B 599 LYS cc_start: 0.7957 (pttm) cc_final: 0.7371 (pttm) REVERT: B 600 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6742 (t) REVERT: B 740 TRP cc_start: 0.7522 (m100) cc_final: 0.7031 (m100) REVERT: B 884 MET cc_start: 0.5461 (mmm) cc_final: 0.5005 (mmm) REVERT: E 123 PHE cc_start: 0.8917 (t80) cc_final: 0.8564 (t80) outliers start: 38 outliers final: 29 residues processed: 299 average time/residue: 0.4974 time to fit residues: 165.4474 Evaluate side-chains 304 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 502 ILE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 680 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 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 600 THR 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 F residue 57 LYS Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 95 ASN 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 204 MET Chi-restraints excluded: chain F residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 164 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 443 ASN B 651 HIS B 718 GLN E 3 HIS F 144 ASN F 200 ASN F 230 ASN F 249 GLN F 278 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.177514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146952 restraints weight = 23081.468| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.59 r_work: 0.3766 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15597 Z= 0.191 Angle : 0.631 9.897 21219 Z= 0.320 Chirality : 0.046 0.269 2269 Planarity : 0.005 0.059 2726 Dihedral : 6.844 82.940 2258 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.86 % Allowed : 22.35 % 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: -0.46 (0.19), residues: 1945 helix: 1.64 (0.27), residues: 398 sheet: -0.72 (0.32), residues: 251 loop : -0.88 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 374 TYR 0.015 0.002 TYR B 580 PHE 0.012 0.002 PHE B 821 TRP 0.020 0.001 TRP B 910 HIS 0.012 0.001 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (15533) covalent geometry : angle 0.62014 / 0.32 (21087) SS BOND : bond 0.00383 / 0.20 ( 54) SS BOND : angle 1.11449 / 0.77 ( 108) hydrogen bonds : bond 0.03713 / 2.57 ( 503) hydrogen bonds : angle 4.72778 / 3.31 ( 1461) Misc. bond : bond 0.11530 / 5.80 ( 2) link_BETA1-4 : bond 0.00543 / 0.29 ( 2) link_BETA1-4 : angle 3.34490 / 1.51 ( 6) link_NAG-ASN : bond 0.00557 / 0.29 ( 6) link_NAG-ASN : angle 2.89472 / 1.91 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.18 seconds wall clock time: 111 minutes 14.41 seconds (6674.41 seconds total)