Starting phenix.real_space_refine on Fri Mar 6 14:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207.map" model { file = "/net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3u_72207/03_2026/9q3u_72207_neut.cif" } resolution = 3.37 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= -0.001 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 19618 2.51 5 N 5099 2.21 5 O 5868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30729 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 8493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8493 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 53, 'TRANS': 1030} Chain breaks: 5 Chain: "C" Number of atoms: 8493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8493 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 53, 'TRANS': 1030} Chain breaks: 5 Chain: "D" Number of atoms: 8493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8493 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 53, 'TRANS': 1030} Chain breaks: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.07, per 1000 atoms: 0.23 Number of scatterers: 30729 At special positions: 0 Unit cell: (149.76, 147.264, 242.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5868 8.00 N 5099 7.00 C 19618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.04 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 287 " - pdb=" SG CYS D 297 " distance=2.03 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 375 " - pdb=" SG CYS D 428 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 476 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 534 " - pdb=" SG CYS D 586 " distance=2.03 Simple disulfide: pdb=" SG CYS D 613 " - pdb=" SG CYS D 645 " distance=2.03 Simple disulfide: pdb=" SG CYS D 658 " - pdb=" SG CYS D 667 " distance=2.03 Simple disulfide: pdb=" SG CYS D 734 " - pdb=" SG CYS D 756 " distance=2.03 Simple disulfide: pdb=" SG CYS D 739 " - pdb=" SG CYS D 745 " distance=2.03 Simple disulfide: pdb=" SG CYS D1028 " - pdb=" SG CYS D1039 " distance=2.03 Simple disulfide: pdb=" SG CYS D1078 " - pdb=" SG CYS D1122 " 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=4, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 298 " " NAG A 703 " - " ASN A 90 " " NAG B1301 " - " ASN B 713 " " NAG B1302 " - " ASN B 797 " " NAG B1304 " - " ASN B1094 " " NAG B1305 " - " ASN B1130 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 278 " " NAG C1305 " - " ASN C 713 " " NAG C1306 " - " ASN C 797 " " NAG C1307 " - " ASN C1070 " " NAG C1308 " - " ASN C1094 " " NAG C1309 " - " ASN C1130 " " NAG D1302 " - " ASN D 278 " " NAG D1303 " - " ASN D 612 " " NAG D1306 " - " ASN D 797 " " NAG D1307 " - " ASN D1070 " " NAG D1308 " - " ASN D1094 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7220 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 47 sheets defined 30.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.776A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.649A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.538A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 219 through 251 removed outlier: 4.116A pdb=" N LYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 4.408A pdb=" N ASP A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.793A pdb=" N SER A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 317 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 364 through 384 removed outlier: 4.068A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 4.392A pdb=" N HIS A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.527A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 4.064A pdb=" N ILE A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.635A pdb=" N CYS A 501 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.532A pdb=" N TYR A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 4.019A pdb=" N GLY A 560 " --> pdb=" O MET A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.543A pdb=" N ALA A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.543A pdb=" N GLN B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.772A pdb=" N VAL B 616 " --> pdb=" O CYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.615A pdb=" N TYR B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.717A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 828 through 838 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 908 through 914 removed outlier: 4.137A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 Processing helix chain 'B' and resid 941 through 961 Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.528A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 3.554A pdb=" N ALA B 985 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 998 " --> pdb=" O THR B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 152 through 155 removed outlier: 4.016A pdb=" N VAL C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.837A pdb=" N VAL C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.752A pdb=" N LEU C 386 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 removed outlier: 3.921A pdb=" N ILE C 406 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 627 through 634 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.651A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 828 through 838 Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 886 removed outlier: 3.659A pdb=" N GLY C 885 " --> pdb=" O TRP C 882 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 886 " --> pdb=" O THR C 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 882 through 886' Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.529A pdb=" N ALA C 899 " --> pdb=" O ALA C 895 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 914 removed outlier: 4.162A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 Processing helix chain 'C' and resid 938 through 940 No H-bonds generated for 'chain 'C' and resid 938 through 940' Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.806A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 978 Processing helix chain 'C' and resid 981 through 1028 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 412 through 418 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 627 through 634 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 742 through 750 Processing helix chain 'D' and resid 751 through 753 No H-bonds generated for 'chain 'D' and resid 751 through 753' Processing helix chain 'D' and resid 754 through 779 removed outlier: 3.564A pdb=" N ASP D 771 " --> pdb=" O ALA D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 822 Processing helix chain 'D' and resid 828 through 838 removed outlier: 3.710A pdb=" N GLN D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 838 " --> pdb=" O GLY D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 881 Processing helix chain 'D' and resid 883 through 887 removed outlier: 4.187A pdb=" N GLY D 887 " --> pdb=" O PHE D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 906 Processing helix chain 'D' and resid 909 through 915 removed outlier: 3.597A pdb=" N TYR D 913 " --> pdb=" O GLN D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 937 Processing helix chain 'D' and resid 941 through 961 removed outlier: 3.511A pdb=" N GLN D 945 " --> pdb=" O LEU D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 980 removed outlier: 3.752A pdb=" N ILE D 976 " --> pdb=" O VAL D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 1028 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.612A pdb=" N TRP A 348 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.886A pdb=" N ALA B 260 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 92 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 223 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N HIS B 203 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N LEU B 219 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL B 33 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.495A pdb=" N PHE B 40 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.958A pdb=" N ASP B 50 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.712A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 164 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 151 removed outlier: 4.505A pdb=" N VAL B 140 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 307 through 315 removed outlier: 5.459A pdb=" N ILE B 308 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 595 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN B 310 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 593 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 312 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 350 through 353 removed outlier: 3.556A pdb=" N LEU B 509 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 428 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 374 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 431 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 372 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 448 through 450 removed outlier: 4.038A pdb=" N TYR B 449 " --> pdb=" O GLN B 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 534 through 539 removed outlier: 3.585A pdb=" N GLY B 544 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.832A pdb=" N SER B 685 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 687 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 671 " --> pdb=" O SER B 687 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB4, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.741A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.550A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AB7, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 27 removed outlier: 3.687A pdb=" N THR C 26 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 87 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 223 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER C 201 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.360A pdb=" N GLY D 562 " --> pdb=" O ASP D 570 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 52 removed outlier: 4.202A pdb=" N ASP C 50 " --> pdb=" O ARG C 269 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR C 270 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP C 286 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 272 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 284 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS C 274 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 114 through 118 removed outlier: 4.126A pdb=" N PHE C 164 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU C 129 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS C 162 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 140 through 143 Processing sheet with id=AC4, first strand: chain 'C' and resid 182 through 185 removed outlier: 4.040A pdb=" N LYS C 183 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 307 through 315 removed outlier: 7.108A pdb=" N VAL C 591 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN C 313 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY C 589 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 350 through 352 Processing sheet with id=AC7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AC8, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AC9, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.175A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 687 " --> pdb=" O GLN C 671 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 666 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 707 through 718 removed outlier: 6.693A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 721 through 724 removed outlier: 4.418A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 731 through 732 Processing sheet with id=AD4, first strand: chain 'C' and resid 783 through 785 Processing sheet with id=AD5, first strand: chain 'C' and resid 1116 through 1118 Processing sheet with id=AD6, first strand: chain 'D' and resid 23 through 27 removed outlier: 9.194A pdb=" N ASN D 58 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR D 265 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA D 259 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA D 260 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 186 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE D 197 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP D 224 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 199 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 45 through 52 removed outlier: 3.962A pdb=" N ASP D 283 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.486A pdb=" N GLY D 100 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 123 through 129 removed outlier: 3.539A pdb=" N SER D 168 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 164 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU D 129 " --> pdb=" O CYS D 162 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS D 162 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 139 through 143 removed outlier: 3.804A pdb=" N ASP D 139 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 141 " --> pdb=" O MET D 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET D 149 " --> pdb=" O TYR D 141 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 307 through 315 removed outlier: 7.033A pdb=" N VAL D 591 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN D 313 " --> pdb=" O GLY D 589 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY D 589 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 321 through 324 removed outlier: 3.804A pdb=" N GLY D 546 " --> pdb=" O VAL D 535 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 350 through 354 removed outlier: 4.118A pdb=" N SER D 510 " --> pdb=" O TYR D 392 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 372 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN D 433 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE D 370 " --> pdb=" O ASN D 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 448 through 449 Processing sheet with id=AE6, first strand: chain 'D' and resid 650 through 651 removed outlier: 3.893A pdb=" N SER D 685 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 673 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 666 " --> pdb=" O ILE D 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 707 through 718 removed outlier: 6.670A pdb=" N SER D 707 " --> pdb=" O THR D1072 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR D1072 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA D 709 " --> pdb=" O ASN D1070 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D1070 " --> pdb=" O ALA D 709 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU D1068 " --> pdb=" O PRO D 711 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR D1063 " --> pdb=" O HIS D1044 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS D1044 " --> pdb=" O TYR D1063 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 707 through 718 removed outlier: 6.670A pdb=" N SER D 707 " --> pdb=" O THR D1072 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR D1072 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA D 709 " --> pdb=" O ASN D1070 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D1070 " --> pdb=" O ALA D 709 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU D1068 " --> pdb=" O PRO D 711 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE D1091 " --> pdb=" O ALA D1074 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 721 through 724 Processing sheet with id=AF1, first strand: chain 'D' and resid 729 through 732 removed outlier: 4.488A pdb=" N LYS D 729 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1116 through 1118 1222 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9823 1.34 - 1.46: 7677 1.46 - 1.58: 13775 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 31471 Sorted by residual: bond pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.413 1.443 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C5 NAG D1302 " pdb=" O5 NAG D1302 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 31466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 42535 2.72 - 5.44: 215 5.44 - 8.15: 15 8.15 - 10.87: 9 10.87 - 13.59: 1 Bond angle restraints: 42775 Sorted by residual: angle pdb=" C ASN B 327 " pdb=" N ILE B 328 " pdb=" CA ILE B 328 " ideal model delta sigma weight residual 121.97 130.29 -8.32 1.80e+00 3.09e-01 2.13e+01 angle pdb=" CA LEU B 299 " pdb=" CB LEU B 299 " pdb=" CG LEU B 299 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" N ILE A 150 " pdb=" CA ILE A 150 " pdb=" C ILE A 150 " ideal model delta sigma weight residual 111.91 108.49 3.42 8.90e-01 1.26e+00 1.48e+01 angle pdb=" N PRO B 557 " pdb=" CA PRO B 557 " pdb=" C PRO B 557 " ideal model delta sigma weight residual 112.47 119.43 -6.96 2.06e+00 2.36e-01 1.14e+01 angle pdb=" CB MET A 454 " pdb=" CG MET A 454 " pdb=" SD MET A 454 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 ... (remaining 42770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16222 17.90 - 35.79: 2082 35.79 - 53.69: 577 53.69 - 71.58: 128 71.58 - 89.48: 50 Dihedral angle restraints: 19059 sinusoidal: 7829 harmonic: 11230 Sorted by residual: dihedral pdb=" CB CYS D1078 " pdb=" SG CYS D1078 " pdb=" SG CYS D1122 " pdb=" CB CYS D1122 " ideal model delta sinusoidal sigma weight residual -86.00 -9.84 -76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual -86.00 -160.22 74.22 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS C 534 " pdb=" SG CYS C 534 " pdb=" SG CYS C 586 " pdb=" CB CYS C 586 " ideal model delta sinusoidal sigma weight residual -86.00 -150.47 64.47 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 19056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4363 0.078 - 0.156: 442 0.156 - 0.234: 7 0.234 - 0.311: 0 0.311 - 0.389: 3 Chirality restraints: 4815 Sorted by residual: chirality pdb=" C2 NAG B1303 " pdb=" C1 NAG B1303 " pdb=" C3 NAG B1303 " pdb=" N2 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 4812 not shown) Planarity restraints: 5507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 567 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" CG ASP B 567 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP B 567 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 567 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 99 " -0.138 9.50e-02 1.11e+02 6.20e-02 2.78e+00 pdb=" NE ARG D 99 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 99 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 99 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 99 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 25 " -0.005 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYR C 25 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 25 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 25 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 25 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 25 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 25 " 0.004 2.00e-02 2.50e+03 ... (remaining 5504 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 14407 2.96 - 3.45: 30229 3.45 - 3.93: 49445 3.93 - 4.42: 55014 4.42 - 4.90: 91394 Nonbonded interactions: 240489 Sorted by model distance: nonbonded pdb=" N GLU C 744 " pdb=" OE1 GLU C 744 " model vdw 2.477 3.120 nonbonded pdb=" OE1 GLN C 800 " pdb=" O6 NAG C1306 " model vdw 2.507 2.432 nonbonded pdb=" OG1 THR D1112 " pdb=" OD1 ASP D1114 " model vdw 2.515 3.040 nonbonded pdb=" O ASN B 327 " pdb=" N THR B 329 " model vdw 2.558 3.120 nonbonded pdb=" N ASP D1114 " pdb=" OD1 ASP D1114 " model vdw 2.593 3.120 ... (remaining 240484 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 'B' selection = (chain 'C' and resid 22 through 1305) selection = (chain 'D' and resid 22 through 1305) } 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: 17.030 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.210 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31533 Z= 0.122 Angle : 0.513 13.588 42909 Z= 0.256 Chirality : 0.043 0.389 4815 Planarity : 0.003 0.062 5489 Dihedral : 17.522 89.479 11719 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 26.82 % Favored : 69.42 % 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: 0.24 (0.14), residues: 3809 helix: 2.13 (0.17), residues: 1029 sheet: 0.02 (0.20), residues: 724 loop : -0.83 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 99 TYR 0.021 0.001 TYR C 25 PHE 0.022 0.001 PHE B 89 TRP 0.019 0.001 TRP B 629 HIS 0.002 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00258 (31471) covalent geometry : angle 0.50875 (42775) SS BOND : bond 0.00165 ( 40) SS BOND : angle 0.80496 ( 80) hydrogen bonds : bond 0.17576 ( 1216) hydrogen bonds : angle 7.55733 ( 3417) Misc. bond : bond 0.00330 ( 4) link_NAG-ASN : bond 0.00248 ( 18) link_NAG-ASN : angle 1.79310 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 151 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.5598 (OUTLIER) cc_final: 0.5037 (m110) REVERT: A 227 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7633 (p-80) REVERT: A 382 MET cc_start: 0.6896 (ptp) cc_final: 0.6446 (ppp) REVERT: A 445 ILE cc_start: 0.7142 (mm) cc_final: 0.6621 (mm) REVERT: A 492 HIS cc_start: 0.3370 (OUTLIER) cc_final: 0.1993 (t-90) REVERT: B 206 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5971 (pt) REVERT: B 238 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6843 (tt) REVERT: B 320 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: B 325 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 373 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.4998 (t80) REVERT: B 391 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7052 (p) REVERT: B 392 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: B 497 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6478 (m-10) REVERT: B 615 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: B 736 MET cc_start: 0.8380 (mmm) cc_final: 0.7892 (tpt) REVERT: C 98 ILE cc_start: 0.6971 (tp) cc_final: 0.6308 (tp) REVERT: C 99 ARG cc_start: 0.6817 (mmt180) cc_final: 0.6049 (mmm160) REVERT: C 153 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8001 (t80) REVERT: C 164 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.5229 (m-10) REVERT: C 166 TYR cc_start: 0.8910 (t80) cc_final: 0.8693 (t80) REVERT: C 187 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: C 212 LEU cc_start: 0.6548 (mt) cc_final: 0.5776 (pp) REVERT: C 330 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6637 (t0) REVERT: C 365 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 433 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6071 (t0) REVERT: C 436 LYS cc_start: 0.1962 (OUTLIER) cc_final: 0.1605 (mtmm) REVERT: C 539 PHE cc_start: 0.6993 (m-10) cc_final: 0.6759 (m-10) REVERT: C 747 ASN cc_start: 0.8809 (m-40) cc_final: 0.8521 (m-40) REVERT: C 965 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8813 (mtpp) REVERT: D 128 CYS cc_start: 0.3441 (OUTLIER) cc_final: 0.2468 (m) REVERT: D 130 PHE cc_start: 0.6366 (m-10) cc_final: 0.6005 (m-80) REVERT: D 173 MET cc_start: 0.3830 (pmm) cc_final: 0.1462 (ptp) REVERT: D 353 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7369 (mmt90) REVERT: D 457 LEU cc_start: 0.1125 (OUTLIER) cc_final: 0.0895 (pp) REVERT: D 946 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8194 (t0) REVERT: D 950 HIS cc_start: 0.8507 (m170) cc_final: 0.8295 (m170) REVERT: D 977 LEU cc_start: 0.8737 (tp) cc_final: 0.7978 (pp) REVERT: D 979 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8050 (ptt-90) REVERT: D 983 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6650 (p) outliers start: 126 outliers final: 94 residues processed: 262 average time/residue: 0.1636 time to fit residues: 73.6517 Evaluate side-chains 267 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 148 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 502 GLN Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1079 HIS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 965 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 728 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 946 ASP Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B 705 ASN B 897 GLN C 184 ASN C 235 GLN C 410 GLN D 339 ASN D 418 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.154860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096284 restraints weight = 72487.922| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.73 r_work: 0.3102 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31533 Z= 0.192 Angle : 0.535 10.223 42909 Z= 0.272 Chirality : 0.043 0.322 4815 Planarity : 0.003 0.041 5489 Dihedral : 7.325 59.712 4898 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 5.58 % Allowed : 25.27 % Favored : 69.15 % 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: 0.16 (0.14), residues: 3809 helix: 2.05 (0.16), residues: 1046 sheet: 0.02 (0.19), residues: 759 loop : -0.93 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 99 TYR 0.026 0.001 TYR B1063 PHE 0.018 0.001 PHE D1117 TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00452 (31471) covalent geometry : angle 0.52860 (42775) SS BOND : bond 0.00214 ( 40) SS BOND : angle 1.06607 ( 80) hydrogen bonds : bond 0.04927 ( 1216) hydrogen bonds : angle 5.77344 ( 3417) Misc. bond : bond 0.00195 ( 4) link_NAG-ASN : bond 0.00316 ( 18) link_NAG-ASN : angle 2.00852 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 152 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.5760 (OUTLIER) cc_final: 0.5170 (m110) REVERT: A 91 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7282 (pp) REVERT: A 337 ASP cc_start: 0.4507 (OUTLIER) cc_final: 0.4065 (t0) REVERT: A 382 MET cc_start: 0.6959 (ptp) cc_final: 0.6550 (ppp) REVERT: A 434 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.3942 (mt-10) REVERT: B 229 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6797 (mp) REVERT: B 320 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: B 325 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7783 (t80) REVERT: B 373 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5144 (t80) REVERT: B 391 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7297 (p) REVERT: B 392 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: B 438 ASP cc_start: 0.6354 (OUTLIER) cc_final: 0.5444 (t70) REVERT: B 497 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: B 686 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8758 (mm-40) REVERT: B 736 MET cc_start: 0.8595 (mmm) cc_final: 0.8127 (tpt) REVERT: B 815 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: B 816 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8131 (t0) REVERT: C 98 ILE cc_start: 0.7010 (tp) cc_final: 0.6343 (tp) REVERT: C 99 ARG cc_start: 0.6878 (mmt180) cc_final: 0.6114 (mmm160) REVERT: C 153 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8058 (t80) REVERT: C 164 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5700 (m-10) REVERT: C 188 PHE cc_start: 0.7934 (m-10) cc_final: 0.7565 (m-10) REVERT: C 212 LEU cc_start: 0.6795 (mt) cc_final: 0.6071 (pp) REVERT: C 235 GLN cc_start: 0.5736 (OUTLIER) cc_final: 0.5094 (mt0) REVERT: C 365 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5779 (m-10) REVERT: C 524 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7310 (mmtt) REVERT: C 539 PHE cc_start: 0.6924 (m-10) cc_final: 0.6708 (m-10) REVERT: C 977 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7931 (mm) REVERT: C 1001 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8802 (mm-40) REVERT: D 128 CYS cc_start: 0.2870 (OUTLIER) cc_final: 0.2036 (m) REVERT: D 130 PHE cc_start: 0.6221 (m-10) cc_final: 0.5829 (m-80) REVERT: D 389 THR cc_start: 0.5082 (OUTLIER) cc_final: 0.4515 (t) REVERT: D 457 LEU cc_start: 0.1161 (OUTLIER) cc_final: 0.0894 (pp) REVERT: D 882 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8612 (p90) REVERT: D 979 ARG cc_start: 0.8266 (mtm110) cc_final: 0.8022 (ptt-90) outliers start: 187 outliers final: 116 residues processed: 322 average time/residue: 0.1599 time to fit residues: 88.3580 Evaluate side-chains 284 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 143 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 686 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 989 ILE Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1079 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 304 optimal weight: 0.0060 chunk 367 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 chunk 325 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.155251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096627 restraints weight = 72714.969| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.47 r_work: 0.3126 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31533 Z= 0.153 Angle : 0.510 12.156 42909 Z= 0.258 Chirality : 0.043 0.317 4815 Planarity : 0.003 0.041 5489 Dihedral : 6.401 59.307 4792 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 5.94 % Allowed : 24.91 % Favored : 69.15 % 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: 0.15 (0.14), residues: 3809 helix: 2.06 (0.16), residues: 1046 sheet: 0.08 (0.19), residues: 738 loop : -0.97 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.033 0.001 TYR D 196 PHE 0.019 0.001 PHE B 558 TRP 0.010 0.001 TRP D 432 HIS 0.003 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00359 (31471) covalent geometry : angle 0.50460 (42775) SS BOND : bond 0.00237 ( 40) SS BOND : angle 0.97974 ( 80) hydrogen bonds : bond 0.04498 ( 1216) hydrogen bonds : angle 5.42375 ( 3417) Misc. bond : bond 0.00192 ( 4) link_NAG-ASN : bond 0.00269 ( 18) link_NAG-ASN : angle 1.98603 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 151 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.5847 (OUTLIER) cc_final: 0.5202 (m110) REVERT: A 91 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7285 (pp) REVERT: A 268 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6397 (t0) REVERT: A 337 ASP cc_start: 0.4404 (OUTLIER) cc_final: 0.3947 (t0) REVERT: A 434 GLU cc_start: 0.4601 (OUTLIER) cc_final: 0.3959 (mt-10) REVERT: A 492 HIS cc_start: 0.3627 (OUTLIER) cc_final: 0.2267 (t-90) REVERT: B 320 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7588 (pp20) REVERT: B 325 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7793 (t80) REVERT: B 373 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5213 (t80) REVERT: B 391 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 392 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: B 438 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.5437 (t70) REVERT: B 497 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: B 514 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5198 (tt) REVERT: B 736 MET cc_start: 0.8582 (mmm) cc_final: 0.8110 (tpt) REVERT: B 815 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: B 816 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8133 (t0) REVERT: C 98 ILE cc_start: 0.6975 (tp) cc_final: 0.6315 (tp) REVERT: C 99 ARG cc_start: 0.6884 (mmt180) cc_final: 0.6048 (mmm160) REVERT: C 149 MET cc_start: 0.7395 (tpp) cc_final: 0.6701 (ttp) REVERT: C 153 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8040 (t80) REVERT: C 164 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5702 (m-10) REVERT: C 212 LEU cc_start: 0.6724 (mt) cc_final: 0.5944 (pp) REVERT: C 365 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.5805 (m-10) REVERT: C 524 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: C 539 PHE cc_start: 0.6932 (m-10) cc_final: 0.6709 (m-10) REVERT: C 977 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7925 (mm) REVERT: C 1001 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8782 (mm-40) REVERT: D 128 CYS cc_start: 0.2671 (OUTLIER) cc_final: 0.1818 (m) REVERT: D 130 PHE cc_start: 0.6175 (m-10) cc_final: 0.5788 (m-80) REVERT: D 267 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: D 389 THR cc_start: 0.4950 (OUTLIER) cc_final: 0.4454 (t) REVERT: D 457 LEU cc_start: 0.1045 (OUTLIER) cc_final: 0.0800 (pp) REVERT: D 882 TRP cc_start: 0.8919 (OUTLIER) cc_final: 0.8570 (p90) REVERT: D 979 ARG cc_start: 0.8274 (mtm110) cc_final: 0.8009 (ptt-90) outliers start: 199 outliers final: 128 residues processed: 328 average time/residue: 0.1632 time to fit residues: 92.3809 Evaluate side-chains 300 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 146 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 91 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 355 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 147 optimal weight: 0.7980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.155980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097626 restraints weight = 72255.555| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.66 r_work: 0.3131 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31533 Z= 0.107 Angle : 0.486 11.659 42909 Z= 0.244 Chirality : 0.042 0.306 4815 Planarity : 0.003 0.041 5489 Dihedral : 6.167 58.493 4779 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 5.34 % Allowed : 25.27 % Favored : 69.39 % 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: 0.26 (0.14), residues: 3809 helix: 2.20 (0.16), residues: 1038 sheet: 0.11 (0.19), residues: 746 loop : -0.90 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.020 0.001 TYR B1063 PHE 0.013 0.001 PHE B 558 TRP 0.009 0.001 TRP D 432 HIS 0.003 0.000 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00244 (31471) covalent geometry : angle 0.48067 (42775) SS BOND : bond 0.00282 ( 40) SS BOND : angle 0.86211 ( 80) hydrogen bonds : bond 0.04007 ( 1216) hydrogen bonds : angle 5.18568 ( 3417) Misc. bond : bond 0.00180 ( 4) link_NAG-ASN : bond 0.00252 ( 18) link_NAG-ASN : angle 1.87866 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 161 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7201 (pp) REVERT: A 248 MET cc_start: 0.0224 (mmt) cc_final: -0.0952 (mtt) REVERT: A 268 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6362 (t0) REVERT: A 337 ASP cc_start: 0.4486 (OUTLIER) cc_final: 0.4024 (t0) REVERT: A 382 MET cc_start: 0.6818 (ptm) cc_final: 0.6603 (ptp) REVERT: A 492 HIS cc_start: 0.3447 (OUTLIER) cc_final: 0.2087 (t-90) REVERT: B 325 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 373 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.5144 (t80) REVERT: B 391 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7309 (p) REVERT: B 392 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: B 438 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.5355 (t70) REVERT: B 497 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: B 686 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8684 (mm-40) REVERT: B 736 MET cc_start: 0.8506 (mmm) cc_final: 0.8035 (tpt) REVERT: B 815 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: B 816 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8097 (t0) REVERT: C 38 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7137 (mtmm) REVERT: C 98 ILE cc_start: 0.6994 (tp) cc_final: 0.6317 (tp) REVERT: C 99 ARG cc_start: 0.6883 (mmt180) cc_final: 0.6029 (mmm160) REVERT: C 149 MET cc_start: 0.7423 (tpp) cc_final: 0.6714 (ttp) REVERT: C 153 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.8011 (t80) REVERT: C 164 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5700 (m-10) REVERT: C 187 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: C 212 LEU cc_start: 0.6658 (mt) cc_final: 0.5940 (pp) REVERT: C 365 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.5774 (m-10) REVERT: C 524 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7296 (mmtt) REVERT: C 539 PHE cc_start: 0.6932 (m-10) cc_final: 0.6721 (m-10) REVERT: C 567 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6534 (t0) REVERT: C 977 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7931 (mm) REVERT: C 1001 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8747 (mm-40) REVERT: D 128 CYS cc_start: 0.2415 (OUTLIER) cc_final: 0.1607 (m) REVERT: D 130 PHE cc_start: 0.6277 (m-10) cc_final: 0.5915 (m-80) REVERT: D 173 MET cc_start: 0.3863 (pmm) cc_final: 0.1578 (ptm) REVERT: D 389 THR cc_start: 0.5079 (OUTLIER) cc_final: 0.4482 (t) REVERT: D 950 HIS cc_start: 0.8556 (m170) cc_final: 0.8342 (m170) REVERT: D 979 ARG cc_start: 0.8258 (mtm110) cc_final: 0.8018 (ptt-90) outliers start: 179 outliers final: 115 residues processed: 322 average time/residue: 0.1662 time to fit residues: 92.0432 Evaluate side-chains 289 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 151 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 686 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 359 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 215 optimal weight: 0.3980 chunk 186 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 371 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097460 restraints weight = 72118.981| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.62 r_work: 0.3128 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31533 Z= 0.113 Angle : 0.497 11.251 42909 Z= 0.247 Chirality : 0.042 0.308 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.922 58.671 4767 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 5.55 % Allowed : 25.24 % Favored : 69.21 % 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: 0.28 (0.14), residues: 3809 helix: 2.17 (0.16), residues: 1045 sheet: 0.15 (0.19), residues: 750 loop : -0.89 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 517 TYR 0.020 0.001 TYR B1063 PHE 0.014 0.001 PHE B 558 TRP 0.013 0.001 TRP A 301 HIS 0.003 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00261 (31471) covalent geometry : angle 0.49226 (42775) SS BOND : bond 0.00188 ( 40) SS BOND : angle 0.84348 ( 80) hydrogen bonds : bond 0.03943 ( 1216) hydrogen bonds : angle 5.09400 ( 3417) Misc. bond : bond 0.00181 ( 4) link_NAG-ASN : bond 0.00238 ( 18) link_NAG-ASN : angle 1.84751 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 155 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7212 (pp) REVERT: A 248 MET cc_start: 0.0147 (mmt) cc_final: -0.1021 (mtt) REVERT: A 268 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6355 (t0) REVERT: A 337 ASP cc_start: 0.4470 (OUTLIER) cc_final: 0.4002 (t0) REVERT: A 382 MET cc_start: 0.6908 (ptm) cc_final: 0.6707 (ptp) REVERT: A 492 HIS cc_start: 0.3521 (OUTLIER) cc_final: 0.2183 (t-90) REVERT: B 320 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: B 325 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 373 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5146 (t80) REVERT: B 391 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7248 (p) REVERT: B 392 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: B 438 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.5367 (t70) REVERT: B 497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: B 686 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8683 (mm-40) REVERT: B 736 MET cc_start: 0.8521 (mmm) cc_final: 0.8045 (tpt) REVERT: B 815 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: B 816 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8097 (t0) REVERT: C 38 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7128 (mtmm) REVERT: C 149 MET cc_start: 0.7400 (tpp) cc_final: 0.6695 (ttp) REVERT: C 153 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.8064 (t80) REVERT: C 164 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5750 (m-10) REVERT: C 187 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: C 212 LEU cc_start: 0.6674 (mt) cc_final: 0.5973 (pp) REVERT: C 330 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6600 (t0) REVERT: C 365 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5881 (m-10) REVERT: C 384 ASN cc_start: 0.7660 (m-40) cc_final: 0.6953 (t0) REVERT: C 520 VAL cc_start: 0.5020 (OUTLIER) cc_final: 0.4624 (p) REVERT: C 524 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7368 (mmtt) REVERT: C 973 LEU cc_start: 0.8493 (tp) cc_final: 0.8269 (tp) REVERT: C 977 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7896 (mm) REVERT: C 1001 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8752 (mm-40) REVERT: D 128 CYS cc_start: 0.2315 (OUTLIER) cc_final: 0.1478 (m) REVERT: D 130 PHE cc_start: 0.6257 (m-10) cc_final: 0.5901 (m-80) REVERT: D 173 MET cc_start: 0.3668 (pmm) cc_final: 0.1514 (ptp) REVERT: D 267 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: D 389 THR cc_start: 0.5044 (OUTLIER) cc_final: 0.4477 (t) REVERT: D 950 HIS cc_start: 0.8544 (m170) cc_final: 0.8316 (m170) REVERT: D 979 ARG cc_start: 0.8253 (mtm110) cc_final: 0.8053 (ptt-90) outliers start: 186 outliers final: 132 residues processed: 320 average time/residue: 0.1605 time to fit residues: 88.6375 Evaluate side-chains 307 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 149 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 686 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 278 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.0010 chunk 76 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 349 optimal weight: 2.9990 chunk 320 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN C1050 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.155468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097937 restraints weight = 72026.970| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.91 r_work: 0.3147 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31533 Z= 0.130 Angle : 0.503 10.654 42909 Z= 0.251 Chirality : 0.042 0.312 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.925 58.413 4763 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 6.12 % Allowed : 24.88 % Favored : 69.00 % 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: 0.26 (0.14), residues: 3809 helix: 2.13 (0.16), residues: 1059 sheet: 0.12 (0.19), residues: 737 loop : -0.90 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.020 0.001 TYR B1063 PHE 0.017 0.001 PHE B 555 TRP 0.009 0.001 TRP D 432 HIS 0.003 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00307 (31471) covalent geometry : angle 0.49736 (42775) SS BOND : bond 0.00184 ( 40) SS BOND : angle 0.97484 ( 80) hydrogen bonds : bond 0.04044 ( 1216) hydrogen bonds : angle 5.03111 ( 3417) Misc. bond : bond 0.00177 ( 4) link_NAG-ASN : bond 0.00229 ( 18) link_NAG-ASN : angle 1.86911 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 153 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7193 (pp) REVERT: A 248 MET cc_start: 0.0149 (mmt) cc_final: -0.0955 (mtt) REVERT: A 268 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6331 (t0) REVERT: A 322 MET cc_start: 0.5366 (mmp) cc_final: 0.3668 (tpp) REVERT: A 337 ASP cc_start: 0.4314 (OUTLIER) cc_final: 0.3856 (t0) REVERT: A 461 MET cc_start: 0.4899 (mmp) cc_final: 0.4024 (ptp) REVERT: A 492 HIS cc_start: 0.3113 (OUTLIER) cc_final: 0.1689 (t-90) REVERT: B 229 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6857 (mp) REVERT: B 320 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7594 (pp20) REVERT: B 325 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7870 (t80) REVERT: B 373 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5210 (t80) REVERT: B 391 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7265 (p) REVERT: B 392 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 438 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.5364 (t70) REVERT: B 497 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: B 514 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5304 (tt) REVERT: B 736 MET cc_start: 0.8471 (mmm) cc_final: 0.7985 (tpt) REVERT: B 815 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 816 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8096 (t0) REVERT: C 38 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7162 (mtmm) REVERT: C 99 ARG cc_start: 0.6817 (mmt180) cc_final: 0.6362 (mmm160) REVERT: C 149 MET cc_start: 0.7420 (tpp) cc_final: 0.6710 (ttp) REVERT: C 153 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8040 (t80) REVERT: C 164 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5797 (m-10) REVERT: C 187 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: C 212 LEU cc_start: 0.6681 (mt) cc_final: 0.5960 (pp) REVERT: C 330 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6596 (t0) REVERT: C 364 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5920 (mt) REVERT: C 365 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: C 384 ASN cc_start: 0.7677 (m-40) cc_final: 0.7013 (t0) REVERT: C 520 VAL cc_start: 0.4912 (OUTLIER) cc_final: 0.4517 (p) REVERT: C 524 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7391 (mmtt) REVERT: C 628 THR cc_start: 0.2297 (OUTLIER) cc_final: 0.2029 (t) REVERT: C 965 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8636 (mtpp) REVERT: C 973 LEU cc_start: 0.8496 (tp) cc_final: 0.8283 (tp) REVERT: C 977 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7896 (mm) REVERT: D 128 CYS cc_start: 0.2336 (OUTLIER) cc_final: 0.1552 (m) REVERT: D 130 PHE cc_start: 0.6186 (m-10) cc_final: 0.5784 (m-80) REVERT: D 267 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: D 389 THR cc_start: 0.5006 (OUTLIER) cc_final: 0.4428 (t) REVERT: D 950 HIS cc_start: 0.8540 (m170) cc_final: 0.8338 (m170) REVERT: D 979 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8072 (ptt-90) outliers start: 205 outliers final: 147 residues processed: 338 average time/residue: 0.1600 time to fit residues: 94.0413 Evaluate side-chains 326 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 149 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 965 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 171 optimal weight: 0.8980 chunk 366 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.155563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097195 restraints weight = 72162.307| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.43 r_work: 0.3116 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31533 Z= 0.129 Angle : 0.507 10.467 42909 Z= 0.252 Chirality : 0.042 0.307 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.893 58.203 4759 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 6.12 % Allowed : 25.00 % Favored : 68.88 % 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: 0.25 (0.14), residues: 3809 helix: 2.09 (0.16), residues: 1062 sheet: 0.12 (0.19), residues: 736 loop : -0.90 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.020 0.001 TYR B1063 PHE 0.018 0.001 PHE B 555 TRP 0.010 0.001 TRP B 629 HIS 0.003 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00303 (31471) covalent geometry : angle 0.50209 (42775) SS BOND : bond 0.00188 ( 40) SS BOND : angle 0.92258 ( 80) hydrogen bonds : bond 0.04024 ( 1216) hydrogen bonds : angle 4.97756 ( 3417) Misc. bond : bond 0.00170 ( 4) link_NAG-ASN : bond 0.00237 ( 18) link_NAG-ASN : angle 1.86925 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 151 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7197 (pp) REVERT: A 248 MET cc_start: 0.0238 (mmt) cc_final: -0.0846 (mtt) REVERT: A 268 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6351 (t0) REVERT: A 337 ASP cc_start: 0.4304 (OUTLIER) cc_final: 0.3836 (t0) REVERT: A 492 HIS cc_start: 0.3074 (OUTLIER) cc_final: 0.1678 (t-90) REVERT: B 203 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7465 (p90) REVERT: B 320 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7594 (pp20) REVERT: B 325 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 373 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5270 (t80) REVERT: B 391 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7359 (p) REVERT: B 392 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: B 438 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.5348 (t70) REVERT: B 497 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: B 514 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5105 (tt) REVERT: B 736 MET cc_start: 0.8501 (mmm) cc_final: 0.8018 (tpt) REVERT: B 815 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: B 816 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8121 (t0) REVERT: C 38 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7211 (mtmm) REVERT: C 149 MET cc_start: 0.7425 (tpp) cc_final: 0.6701 (ttp) REVERT: C 153 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8040 (t80) REVERT: C 164 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5699 (m-10) REVERT: C 187 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: C 212 LEU cc_start: 0.6736 (mt) cc_final: 0.5991 (pp) REVERT: C 330 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6611 (t0) REVERT: C 364 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5991 (mt) REVERT: C 365 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.5787 (m-10) REVERT: C 384 ASN cc_start: 0.7723 (m-40) cc_final: 0.6977 (t0) REVERT: C 520 VAL cc_start: 0.4885 (OUTLIER) cc_final: 0.4487 (p) REVERT: C 524 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7400 (mmtt) REVERT: C 628 THR cc_start: 0.2261 (OUTLIER) cc_final: 0.1995 (t) REVERT: C 965 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8619 (mtpp) REVERT: C 977 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7949 (mm) REVERT: D 128 CYS cc_start: 0.2351 (OUTLIER) cc_final: 0.1529 (m) REVERT: D 130 PHE cc_start: 0.6187 (m-10) cc_final: 0.5795 (m-80) REVERT: D 173 MET cc_start: 0.3772 (pmm) cc_final: 0.1588 (ptp) REVERT: D 267 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: D 389 THR cc_start: 0.4960 (OUTLIER) cc_final: 0.4371 (t) REVERT: D 509 LEU cc_start: 0.6538 (mp) cc_final: 0.6179 (pp) REVERT: D 979 ARG cc_start: 0.8286 (mtm110) cc_final: 0.8079 (ptt-90) outliers start: 205 outliers final: 153 residues processed: 337 average time/residue: 0.1588 time to fit residues: 92.8585 Evaluate side-chains 330 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 147 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 933 SER Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 965 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 45 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 335 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 370 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.155866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097840 restraints weight = 72657.776| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.88 r_work: 0.3154 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31533 Z= 0.111 Angle : 0.499 10.208 42909 Z= 0.247 Chirality : 0.042 0.301 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.851 58.304 4759 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 5.58 % Allowed : 25.48 % Favored : 68.94 % 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: 0.26 (0.14), residues: 3809 helix: 2.11 (0.16), residues: 1058 sheet: 0.15 (0.19), residues: 749 loop : -0.91 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.019 0.001 TYR B1063 PHE 0.017 0.001 PHE B 555 TRP 0.011 0.001 TRP B 629 HIS 0.003 0.000 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00257 (31471) covalent geometry : angle 0.49422 (42775) SS BOND : bond 0.00160 ( 40) SS BOND : angle 0.86010 ( 80) hydrogen bonds : bond 0.03824 ( 1216) hydrogen bonds : angle 4.89648 ( 3417) Misc. bond : bond 0.00161 ( 4) link_NAG-ASN : bond 0.00229 ( 18) link_NAG-ASN : angle 1.81354 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 152 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7195 (pp) REVERT: A 248 MET cc_start: 0.0231 (mmt) cc_final: -0.0852 (mtt) REVERT: A 268 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6342 (t0) REVERT: A 322 MET cc_start: 0.5215 (mmp) cc_final: 0.3639 (tpp) REVERT: A 337 ASP cc_start: 0.4242 (OUTLIER) cc_final: 0.3802 (t0) REVERT: A 461 MET cc_start: 0.4838 (mmp) cc_final: 0.4198 (ptp) REVERT: A 492 HIS cc_start: 0.3169 (OUTLIER) cc_final: 0.1786 (t-90) REVERT: A 581 LYS cc_start: 0.6704 (tptp) cc_final: 0.5942 (tttp) REVERT: B 103 PHE cc_start: 0.7089 (m-80) cc_final: 0.6869 (m-80) REVERT: B 203 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7427 (p90) REVERT: B 320 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: B 325 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7880 (t80) REVERT: B 373 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5254 (t80) REVERT: B 391 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7376 (p) REVERT: B 392 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 438 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5331 (t70) REVERT: B 497 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.6504 (m-10) REVERT: B 514 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5274 (tt) REVERT: B 686 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8708 (mm-40) REVERT: B 736 MET cc_start: 0.8448 (mmm) cc_final: 0.7963 (tpt) REVERT: B 815 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: B 816 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8087 (t0) REVERT: C 38 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7143 (mtmm) REVERT: C 99 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6544 (mmm160) REVERT: C 149 MET cc_start: 0.7426 (tpp) cc_final: 0.6717 (ttp) REVERT: C 153 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (t80) REVERT: C 164 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5656 (m-10) REVERT: C 187 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: C 212 LEU cc_start: 0.6681 (mt) cc_final: 0.5931 (pp) REVERT: C 364 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5943 (mt) REVERT: C 365 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5760 (m-10) REVERT: C 384 ASN cc_start: 0.7716 (m-40) cc_final: 0.7020 (t0) REVERT: C 520 VAL cc_start: 0.4739 (OUTLIER) cc_final: 0.4325 (p) REVERT: C 524 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7399 (mmtt) REVERT: C 628 THR cc_start: 0.2371 (OUTLIER) cc_final: 0.2098 (t) REVERT: C 965 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8614 (mtpp) REVERT: C 977 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7887 (mm) REVERT: D 130 PHE cc_start: 0.6178 (m-10) cc_final: 0.5939 (m-80) REVERT: D 173 MET cc_start: 0.3666 (pmm) cc_final: 0.1477 (ptp) REVERT: D 267 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: D 389 THR cc_start: 0.4997 (OUTLIER) cc_final: 0.4389 (t) REVERT: D 509 LEU cc_start: 0.6519 (mp) cc_final: 0.6219 (pt) REVERT: D 578 LEU cc_start: 0.9084 (mm) cc_final: 0.8297 (tp) outliers start: 187 outliers final: 143 residues processed: 322 average time/residue: 0.1631 time to fit residues: 90.4529 Evaluate side-chains 317 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 145 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 686 GLN Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 933 SER Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 965 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 969 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 364 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 331 optimal weight: 1.9990 chunk 381 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 239 optimal weight: 0.5980 chunk 320 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097619 restraints weight = 72341.222| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.60 r_work: 0.3136 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31533 Z= 0.106 Angle : 0.495 10.219 42909 Z= 0.245 Chirality : 0.042 0.303 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.813 58.802 4759 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 5.43 % Allowed : 25.54 % Favored : 69.03 % 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: 0.29 (0.14), residues: 3809 helix: 2.13 (0.16), residues: 1058 sheet: 0.19 (0.19), residues: 739 loop : -0.89 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.019 0.001 TYR B1063 PHE 0.015 0.001 PHE C 188 TRP 0.011 0.001 TRP B 629 HIS 0.002 0.000 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00247 (31471) covalent geometry : angle 0.49081 (42775) SS BOND : bond 0.00163 ( 40) SS BOND : angle 0.85631 ( 80) hydrogen bonds : bond 0.03742 ( 1216) hydrogen bonds : angle 4.84125 ( 3417) Misc. bond : bond 0.00153 ( 4) link_NAG-ASN : bond 0.00229 ( 18) link_NAG-ASN : angle 1.77539 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 150 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7226 (pp) REVERT: A 248 MET cc_start: 0.0086 (mmt) cc_final: -0.0981 (mtt) REVERT: A 268 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6339 (t0) REVERT: A 322 MET cc_start: 0.5262 (mmp) cc_final: 0.3627 (tpp) REVERT: A 337 ASP cc_start: 0.4444 (OUTLIER) cc_final: 0.3982 (t0) REVERT: A 492 HIS cc_start: 0.3113 (OUTLIER) cc_final: 0.1648 (t-90) REVERT: A 581 LYS cc_start: 0.6726 (tptp) cc_final: 0.5980 (tttp) REVERT: B 103 PHE cc_start: 0.7152 (m-80) cc_final: 0.6945 (m-80) REVERT: B 203 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7559 (p90) REVERT: B 320 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: B 325 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7885 (t80) REVERT: B 373 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5304 (t80) REVERT: B 391 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 392 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: B 438 ASP cc_start: 0.6276 (OUTLIER) cc_final: 0.5357 (t70) REVERT: B 497 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: B 514 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5381 (tt) REVERT: B 686 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (mm-40) REVERT: B 736 MET cc_start: 0.8454 (mmm) cc_final: 0.7971 (tpt) REVERT: B 815 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: B 816 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8088 (t0) REVERT: C 38 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7133 (mtmm) REVERT: C 99 ARG cc_start: 0.7363 (mmt180) cc_final: 0.6602 (mmm160) REVERT: C 149 MET cc_start: 0.7435 (tpp) cc_final: 0.6732 (ttp) REVERT: C 153 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 164 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5749 (m-10) REVERT: C 187 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: C 212 LEU cc_start: 0.6662 (mt) cc_final: 0.5903 (pp) REVERT: C 364 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5941 (mt) REVERT: C 365 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5832 (m-10) REVERT: C 384 ASN cc_start: 0.7692 (m-40) cc_final: 0.7068 (t0) REVERT: C 520 VAL cc_start: 0.4667 (OUTLIER) cc_final: 0.4263 (p) REVERT: C 524 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7378 (mmtt) REVERT: C 628 THR cc_start: 0.2306 (OUTLIER) cc_final: 0.2038 (t) REVERT: C 977 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7783 (mm) REVERT: C 996 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8512 (mtt180) REVERT: C 1137 LEU cc_start: 0.8851 (mp) cc_final: 0.8549 (tt) REVERT: D 130 PHE cc_start: 0.6152 (m-10) cc_final: 0.5934 (m-80) REVERT: D 173 MET cc_start: 0.3577 (pmm) cc_final: 0.1493 (ptp) REVERT: D 267 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: D 389 THR cc_start: 0.5018 (OUTLIER) cc_final: 0.4425 (t) REVERT: D 509 LEU cc_start: 0.6513 (mp) cc_final: 0.6241 (pt) REVERT: D 578 LEU cc_start: 0.9125 (mm) cc_final: 0.8328 (tp) outliers start: 182 outliers final: 142 residues processed: 315 average time/residue: 0.1624 time to fit residues: 88.3693 Evaluate side-chains 320 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 149 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 686 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 933 SER Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 54 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 357 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 317 GLN B 677 HIS C 235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.154252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095093 restraints weight = 72422.073| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.28 r_work: 0.3108 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31533 Z= 0.196 Angle : 0.557 10.041 42909 Z= 0.279 Chirality : 0.044 0.322 4815 Planarity : 0.003 0.042 5489 Dihedral : 6.003 59.342 4752 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 5.43 % Allowed : 25.48 % Favored : 69.09 % 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: 0.14 (0.14), residues: 3809 helix: 1.97 (0.16), residues: 1066 sheet: 0.02 (0.19), residues: 735 loop : -0.93 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.022 0.001 TYR B1063 PHE 0.020 0.001 PHE B 555 TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00469 (31471) covalent geometry : angle 0.55112 (42775) SS BOND : bond 0.00219 ( 40) SS BOND : angle 1.16871 ( 80) hydrogen bonds : bond 0.04586 ( 1216) hydrogen bonds : angle 5.04671 ( 3417) Misc. bond : bond 0.00166 ( 4) link_NAG-ASN : bond 0.00277 ( 18) link_NAG-ASN : angle 2.05189 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 148 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.5880 (OUTLIER) cc_final: 0.5068 (m110) REVERT: A 91 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7255 (pp) REVERT: A 248 MET cc_start: 0.0055 (mmt) cc_final: -0.0976 (mtt) REVERT: A 268 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6244 (t0) REVERT: A 322 MET cc_start: 0.5412 (mmp) cc_final: 0.3869 (tpp) REVERT: A 337 ASP cc_start: 0.4347 (OUTLIER) cc_final: 0.3862 (t0) REVERT: A 461 MET cc_start: 0.5125 (mmp) cc_final: 0.4162 (ptp) REVERT: A 492 HIS cc_start: 0.2866 (OUTLIER) cc_final: 0.1504 (t-90) REVERT: B 203 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (p90) REVERT: B 320 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: B 325 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 373 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5433 (t80) REVERT: B 391 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7338 (p) REVERT: B 392 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: B 438 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.5430 (t70) REVERT: B 497 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: B 514 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5397 (tt) REVERT: B 736 MET cc_start: 0.8612 (mmm) cc_final: 0.8110 (tpt) REVERT: B 815 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: B 816 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8121 (t0) REVERT: C 153 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 164 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5835 (m-10) REVERT: C 187 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: C 364 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.6026 (mt) REVERT: C 365 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.5880 (m-10) REVERT: C 384 ASN cc_start: 0.7658 (m-40) cc_final: 0.7025 (t0) REVERT: C 520 VAL cc_start: 0.4688 (OUTLIER) cc_final: 0.4271 (p) REVERT: C 524 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.6900 (mttt) REVERT: C 965 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: C 977 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7773 (mm) REVERT: C 1001 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8766 (mm-40) REVERT: D 101 TRP cc_start: 0.7387 (p-90) cc_final: 0.7176 (p-90) REVERT: D 173 MET cc_start: 0.3506 (pmm) cc_final: 0.1436 (ptp) REVERT: D 389 THR cc_start: 0.4884 (OUTLIER) cc_final: 0.4283 (t) REVERT: D 509 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6188 (pt) REVERT: D 1079 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7752 (p-80) outliers start: 182 outliers final: 143 residues processed: 314 average time/residue: 0.1578 time to fit residues: 86.3095 Evaluate side-chains 315 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 144 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 955 LEU Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 76 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 933 SER Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 955 LEU Chi-restraints excluded: chain C residue 965 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 871 SER Chi-restraints excluded: chain D residue 930 ILE Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1079 HIS Chi-restraints excluded: chain D residue 1132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 128 optimal weight: 0.7980 chunk 139 optimal weight: 0.0370 chunk 369 optimal weight: 0.9980 chunk 363 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 339 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 377 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 292 optimal weight: 9.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.155723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097831 restraints weight = 72506.820| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.75 r_work: 0.3121 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31533 Z= 0.108 Angle : 0.509 9.996 42909 Z= 0.253 Chirality : 0.043 0.310 4815 Planarity : 0.003 0.041 5489 Dihedral : 5.836 58.144 4751 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 4.59 % Allowed : 26.34 % Favored : 69.06 % 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 (0.14), residues: 3809 helix: 2.12 (0.16), residues: 1046 sheet: 0.13 (0.19), residues: 746 loop : -0.92 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.019 0.001 TYR B1063 PHE 0.033 0.001 PHE A 399 TRP 0.014 0.001 TRP B 629 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00251 (31471) covalent geometry : angle 0.50353 (42775) SS BOND : bond 0.00173 ( 40) SS BOND : angle 0.88704 ( 80) hydrogen bonds : bond 0.03923 ( 1216) hydrogen bonds : angle 4.87904 ( 3417) Misc. bond : bond 0.00148 ( 4) link_NAG-ASN : bond 0.00246 ( 18) link_NAG-ASN : angle 1.88628 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9342.48 seconds wall clock time: 160 minutes 9.46 seconds (9609.46 seconds total)