Starting phenix.real_space_refine on Sun Aug 9 10:00:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygo_72936/08_2026/9ygo_72936.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 182 5.16 5 C 21050 2.51 5 N 5423 2.21 5 O 6429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33084 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9229 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1134} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 9162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9162 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 49, 'TRANS': 1124} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 9215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9215 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1129} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 906 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 906 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 Time building chain proxies: 7.21, per 1000 atoms: 0.22 Number of scatterers: 33084 At special positions: 0 Unit cell: (149.04, 157.32, 222.64, 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 182 16.00 O 6429 8.00 N 5423 7.00 C 21050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.02 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=1.75 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.14 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.04 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Atom "HETATM32970 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1401 " - " ASN A 58 " " NAG A1402 " - " ASN A 433 " " NAG A1403 " - " ASN A 454 " " NAG A1404 " - " ASN A 664 " " NAG A1405 " - " ASN A 703 " " NAG A1406 " - " ASN A 725 " " NAG A1407 " - " ASN A 793 " " NAG B1401 " - " ASN B 664 " " NAG B1402 " - " ASN B 725 " " NAG B1403 " - " ASN B 793 " " NAG B1404 " - " ASN B1211 " " NAG B1405 " - " ASN B 132 " " NAG B1406 " - " ASN B 188 " " NAG C1401 " - " ASN C 58 " " NAG C1402 " - " ASN C 335 " " NAG C1403 " - " ASN C 433 " " NAG C1404 " - " ASN C 454 " " NAG C1405 " - " ASN C 664 " " NAG C1406 " - " ASN C 725 " " NAG C1407 " - " ASN C 793 " " NAG C1408 " - " ASN C1211 " " NAG C1409 " - " ASN C 188 " " NAG K 1 " - " ASN A 335 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7906 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 85 sheets defined 22.2% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.826A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.047A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.659A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.779A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.608A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.686A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.907A pdb=" N THR A 527 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 removed outlier: 5.010A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.910A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.520A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.733A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.759A pdb=" N LEU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.929A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.782A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 4.097A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.661A pdb=" N GLN A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.510A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A1045 " --> pdb=" O ASN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 Processing helix chain 'A' and resid 1058 through 1065 removed outlier: 3.825A pdb=" N LEU A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A1063 " --> pdb=" O GLN A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.910A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A1099 " --> pdb=" O ASP A1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 4.387A pdb=" N LEU B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.986A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.685A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.560A pdb=" N PHE B 817 " --> pdb=" O ASP B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.772A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 862 Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.110A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.512A pdb=" N LEU B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.995A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.998A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.569A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 removed outlier: 3.850A pdb=" N ILE B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.698A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.860A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 4.122A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B1099 " --> pdb=" O ASP B1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.949A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.878A pdb=" N GLY C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.622A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 4.131A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.615A pdb=" N PHE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.652A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 862 removed outlier: 3.558A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET C 862 " --> pdb=" O ALA C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 901 through 909 removed outlier: 4.014A pdb=" N LEU C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 927 removed outlier: 3.542A pdb=" N GLU C 920 " --> pdb=" O VAL C 916 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS C 925 " --> pdb=" O ALA C 921 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR C 926 " --> pdb=" O TYR C 922 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.508A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 991 removed outlier: 3.605A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.903A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.649A pdb=" N SER C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.559A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1061 removed outlier: 3.537A pdb=" N GLU C1060 " --> pdb=" O SER C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 5.120A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.700A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.564A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 29 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.723A pdb=" N GLU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 29 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.548A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 5.803A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 75 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 61 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 59 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 removed outlier: 5.803A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 75 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TRP A 257 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 105 " --> pdb=" O TRP A 257 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 259 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 202 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.601A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.965A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 113 removed outlier: 4.045A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 111 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 118 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 7.582A pdb=" N LEU A 146 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN A 188 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 148 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS A 186 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 150 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.546A pdb=" N GLY A 302 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.989A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 371 removed outlier: 4.065A pdb=" N HIS A 364 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N CYS A 370 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 422 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 586 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.553A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB6, first strand: chain 'A' and resid 620 through 624 removed outlier: 3.869A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.227A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 791 removed outlier: 3.597A pdb=" N VAL A1156 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A1177 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 803 removed outlier: 4.237A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.414A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.894A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.810A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 1170 through 1172 removed outlier: 3.578A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.440A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 658 " --> pdb=" O TYR C 667 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.707A pdb=" N LEU B 261 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.526A pdb=" N GLY B 65 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 80 through 81 removed outlier: 4.050A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.576A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 189 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.906A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 removed outlier: 4.076A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 595 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 349 removed outlier: 4.076A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 595 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.883A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE1, first strand: chain 'B' and resid 620 through 622 Processing sheet with id=AE2, first strand: chain 'B' and resid 713 through 714 Processing sheet with id=AE3, first strand: chain 'B' and resid 730 through 731 removed outlier: 6.601A pdb=" N THR B 766 " --> pdb=" O VAL B 731 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'B' and resid 745 through 746 Processing sheet with id=AE5, first strand: chain 'B' and resid 786 through 791 removed outlier: 3.765A pdb=" N VAL B1156 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 794 through 803 removed outlier: 3.991A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.446A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 866 through 868 Processing sheet with id=AE9, first strand: chain 'B' and resid 1162 through 1163 Processing sheet with id=AF1, first strand: chain 'B' and resid 1169 through 1172 removed outlier: 3.889A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF3, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.852A pdb=" N ARG C 34 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.852A pdb=" N ARG C 34 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 199 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 203 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.102A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.547A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 111 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 113 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 183 through 190 removed outlier: 4.199A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 125 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 305 removed outlier: 3.627A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 338 removed outlier: 5.973A pdb=" N THR C 435 " --> pdb=" O VAL C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 4.172A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 347 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 388 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 586 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 467 through 468 removed outlier: 4.164A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG6, first strand: chain 'C' and resid 620 through 624 removed outlier: 4.056A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.701A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 786 through 791 Processing sheet with id=AG9, first strand: chain 'C' and resid 794 through 796 Processing sheet with id=AH1, first strand: chain 'C' and resid 794 through 796 removed outlier: 3.549A pdb=" N GLY C1140 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.447A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.641A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1175 through 1180 Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.721A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.633A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AH8, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.606A pdb=" N LEU I 20 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP I 72 " --> pdb=" O HIS I 77 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AI1, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 94 through 95 Processing sheet with id=AI3, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.541A pdb=" N GLN J 5 " --> pdb=" O SER J 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.552A pdb=" N THR J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.840A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.840A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AI8, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.678A pdb=" N GLY M 13 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR M 34 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.678A pdb=" N GLY M 13 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.870A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE M 75 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.858A pdb=" N ALA N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR N 34 " --> pdb=" O ALA N 89 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.858A pdb=" N ALA N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 19 through 24 1099 hydrogen bonds defined for protein. 2934 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: 10.30 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9694 1.34 - 1.46: 8570 1.46 - 1.58: 15414 1.58 - 1.71: 0 1.71 - 1.83: 208 Bond restraints: 33886 Sorted by residual: bond pdb=" N SER C 340 " pdb=" CA SER C 340 " ideal model delta sigma weight residual 1.453 1.490 -0.036 9.20e-03 1.18e+04 1.56e+01 bond pdb=" N CYS B 292 " pdb=" CA CYS B 292 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.19e-02 7.06e+03 1.38e+01 bond pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N LEU B 748 " pdb=" CA LEU B 748 " ideal model delta sigma weight residual 1.453 1.491 -0.039 1.18e-02 7.18e+03 1.07e+01 bond pdb=" N VAL B 677 " pdb=" CA VAL B 677 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 ... (remaining 33881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 45204 2.46 - 4.92: 852 4.92 - 7.38: 75 7.38 - 9.83: 28 9.83 - 12.29: 5 Bond angle restraints: 46164 Sorted by residual: angle pdb=" C ASN C 58 " pdb=" CA ASN C 58 " pdb=" CB ASN C 58 " ideal model delta sigma weight residual 111.86 118.42 -6.56 1.34e+00 5.57e-01 2.40e+01 angle pdb=" C PHE A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" CB LYS A1200 " pdb=" CG LYS A1200 " pdb=" CD LYS A1200 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" O ASN C 725 " pdb=" C ASN C 725 " pdb=" N LEU C 726 " ideal model delta sigma weight residual 122.68 128.19 -5.51 1.27e+00 6.20e-01 1.89e+01 angle pdb=" N THR B 133 " pdb=" CA THR B 133 " pdb=" C THR B 133 " ideal model delta sigma weight residual 113.41 108.26 5.15 1.22e+00 6.72e-01 1.78e+01 ... (remaining 46159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 18724 17.70 - 35.40: 1326 35.40 - 53.10: 262 53.10 - 70.80: 44 70.80 - 88.50: 14 Dihedral angle restraints: 20370 sinusoidal: 8037 harmonic: 12333 Sorted by residual: dihedral pdb=" CB CYS C 734 " pdb=" SG CYS C 734 " pdb=" SG CYS C 743 " pdb=" CB CYS C 743 " ideal model delta sinusoidal sigma weight residual 93.00 151.91 -58.91 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 495 " pdb=" CB CYS C 495 " ideal model delta sinusoidal sigma weight residual 93.00 146.71 -53.71 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS B 20 " pdb=" SG CYS B 20 " pdb=" SG CYS B 156 " pdb=" CB CYS B 156 " ideal model delta sinusoidal sigma weight residual 93.00 142.58 -49.58 1 1.00e+01 1.00e-02 3.38e+01 ... (remaining 20367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4980 0.109 - 0.218: 262 0.218 - 0.328: 11 0.328 - 0.437: 5 0.437 - 0.546: 1 Chirality restraints: 5259 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.73e+01 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 725 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 5256 not shown) Planarity restraints: 5920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1406 " -0.332 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG C1406 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C1406 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C1406 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG C1406 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " -0.269 2.00e-02 2.50e+03 2.25e-01 6.35e+02 pdb=" C7 NAG B1401 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " 0.379 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.203 2.00e-02 2.50e+03 1.68e-01 3.55e+02 pdb=" C7 NAG B1402 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.018 2.00e-02 2.50e+03 ... (remaining 5917 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 13042 2.89 - 3.40: 30559 3.40 - 3.90: 54648 3.90 - 4.40: 60504 4.40 - 4.90: 102476 Nonbonded interactions: 261229 Sorted by model distance: nonbonded pdb=" O SER A 651 " pdb=" CD1 LEU C 61 " model vdw 2.393 3.460 nonbonded pdb=" ND2 ASN C 343 " pdb=" O ASN C 437 " model vdw 2.422 3.120 nonbonded pdb=" O PHE B 18 " pdb=" SG CYS B 156 " model vdw 2.427 3.400 nonbonded pdb=" CB GLU C 272 " pdb=" C8 NAG C1401 " model vdw 2.433 3.860 nonbonded pdb=" O ASN H 31 " pdb=" OD1 ASN H 31 " model vdw 2.452 3.040 ... (remaining 261224 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 'A' and (resid 14 through 146 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 163 or (resid 164 and (name N o \ r name CA or name C or name O or name CB )) or resid 165 or (resid 166 and (name \ N or name CA or name C or name O or name CB )) or resid 167 through 235 or resi \ d 254 through 271 or (resid 272 and (name N or name CA or name C or name O or na \ me CB )) or resid 273 through 311 or (resid 312 and (name N or name CA or name C \ or name O or name CB )) or resid 313 through 322 or resid 326 through 606 or re \ sid 609 through 660 or (resid 661 and (name N or name CA or name C or name O or \ name CB )) or resid 662 through 1065 or (resid 1066 and (name N or name CA or na \ me C or name O or name CB )) or resid 1067 through 1406)) selection = (chain 'B' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 163 or (resid 164 \ and (name N or name CA or name C or name O or name CB )) or resid 165 or (resid \ 166 and (name N or name CA or name C or name O or name CB )) or resid 167 throug \ h 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 205 or (resid 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 through 235 or resid 254 through 271 or (resid 272 and \ (name N or name CA or name C or name O or name CB )) or resid 273 through 779 o \ r (resid 780 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 81 through 1153 or (resid 1154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1155 through 1406)) selection = (chain 'C' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 235 or resid 254 through 311 or (resid 312 and (name N or name CA \ or name C or name O or name CB )) or resid 313 through 322 or resid 326 through \ 606 or resid 609 through 660 or (resid 661 and (name N or name CA or name C or n \ ame O or name CB )) or resid 662 through 779 or (resid 780 and (name N or name C \ A or name C or name O or name CB )) or resid 781 through 931 or (resid 932 and ( \ name N or name CA or name C or name O or name CB )) or resid 933 through 1065 or \ (resid 1066 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 067 through 1153 or (resid 1154 and (name N or name CA or name C or name O or na \ me CB )) or resid 1155 through 1406)) } ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 2 through 62 or (resid 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 112)) selection = (chain 'J' and (resid 2 through 62 or (resid 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 112)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.920 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 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 : 0.005 0.282 33962 Z= 0.309 Angle : 0.840 33.392 46340 Z= 0.482 Chirality : 0.053 0.546 5259 Planarity : 0.007 0.283 5897 Dihedral : 12.471 88.499 12308 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.26 % Allowed : 16.54 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 4183 helix: 0.86 (0.20), residues: 689 sheet: -0.24 (0.18), residues: 893 loop : -1.65 (0.11), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 447 TYR 0.046 0.001 TYR A 266 PHE 0.032 0.001 PHE B 940 TRP 0.052 0.002 TRP B 644 HIS 0.009 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.30 (33886) covalent geometry : angle 0.78491 / 0.47 (46164) SS BOND : bond 0.04219 / 1.77 ( 52) SS BOND : angle 3.30992 / 2.81 ( 104) hydrogen bonds : bond 0.24147 / 16.11 ( 1061) hydrogen bonds : angle 8.54923 / 5.73 ( 2934) link_BETA1-4 : bond 0.00417 / 0.22 ( 1) link_BETA1-4 : angle 0.43545 / 0.23 ( 3) link_NAG-ASN : bond 0.00721 / 0.34 ( 23) link_NAG-ASN : angle 6.69524 / 5.52 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 663 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.1097 (ppp) cc_final: 0.0191 (ttm) REVERT: A 360 LEU cc_start: 0.8751 (mm) cc_final: 0.8504 (mt) REVERT: A 387 THR cc_start: 0.9202 (m) cc_final: 0.8978 (p) REVERT: A 553 GLU cc_start: 0.7799 (pm20) cc_final: 0.7172 (mt-10) REVERT: A 578 ASP cc_start: 0.7991 (t0) cc_final: 0.6946 (t0) REVERT: A 632 ILE cc_start: 0.8721 (mm) cc_final: 0.8391 (mt) REVERT: A 691 LEU cc_start: 0.6233 (tp) cc_final: 0.5763 (tt) REVERT: A 835 PHE cc_start: 0.7708 (t80) cc_final: 0.7099 (t80) REVERT: A 1126 ASN cc_start: 0.7635 (m-40) cc_final: 0.6838 (p0) REVERT: A 1205 MET cc_start: 0.2598 (mmp) cc_final: 0.1947 (mmt) REVERT: B 149 THR cc_start: 0.7304 (p) cc_final: 0.6954 (p) REVERT: B 240 LEU cc_start: 0.6488 (tp) cc_final: 0.6257 (mt) REVERT: B 573 LEU cc_start: 0.2789 (OUTLIER) cc_final: 0.2495 (mp) REVERT: B 649 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6029 (t80) REVERT: B 821 ASN cc_start: 0.7008 (m-40) cc_final: 0.6725 (m-40) REVERT: B 854 GLN cc_start: 0.7537 (mm110) cc_final: 0.7312 (mt0) REVERT: B 1126 ASN cc_start: 0.7259 (m-40) cc_final: 0.7027 (m-40) REVERT: B 1168 ARG cc_start: 0.3005 (ppt170) cc_final: 0.1566 (tmm-80) REVERT: B 1172 PRO cc_start: 0.6748 (Cg_endo) cc_final: 0.6330 (Cg_exo) REVERT: C 301 THR cc_start: 0.8857 (m) cc_final: 0.8512 (p) REVERT: C 461 VAL cc_start: 0.8938 (t) cc_final: 0.8643 (t) REVERT: C 971 TRP cc_start: 0.6176 (m-90) cc_final: 0.5839 (m-90) REVERT: C 1008 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4969 (t80) REVERT: C 1095 ASP cc_start: 0.7284 (m-30) cc_final: 0.6983 (m-30) REVERT: C 1205 MET cc_start: -0.0469 (tpt) cc_final: -0.1371 (mmm) REVERT: H 69 LEU cc_start: 0.0320 (mp) cc_final: 0.0047 (tp) REVERT: M 35 TRP cc_start: 0.6220 (m100) cc_final: 0.5804 (m100) REVERT: M 45 LYS cc_start: 0.7777 (tttt) cc_final: 0.7301 (mmmt) REVERT: M 60 ASP cc_start: 0.7620 (p0) cc_final: 0.7385 (p0) outliers start: 47 outliers final: 22 residues processed: 699 average time/residue: 0.2060 time to fit residues: 240.6220 Evaluate side-chains 461 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 436 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.0270 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 overall best weight: 0.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 201 HIS A 291 GLN A 465 HIS A 535 GLN A 605 ASN A 643 ASN A 799 HIS A 847 ASN A 863 GLN A 872 ASN A 954 GLN A1034 ASN A1071 GLN A1122 ASN A1174 GLN A1201 ASN A1211 ASN B 100 ASN B 243 ASN B 364 HIS ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 GLN B 552 ASN B 646 ASN B 683 GLN B 702 ASN B 804 GLN B 881 ASN B 954 GLN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1030 GLN C 53 ASN C 265 GLN C 291 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN C 643 ASN C 847 ASN C 854 GLN C 856 GLN C 988 ASN C1017 ASN C1038 GLN C1073 GLN H 3 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95AASN N 6 GLN N 37 GLN N 95AASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.202377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.174807 restraints weight = 60523.009| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.35 r_work: 0.4016 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33962 Z= 0.125 Angle : 0.617 19.876 46340 Z= 0.308 Chirality : 0.044 0.222 5259 Planarity : 0.004 0.068 5897 Dihedral : 5.409 80.444 5097 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.71 % Allowed : 16.05 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4183 helix: 1.21 (0.20), residues: 705 sheet: -0.27 (0.16), residues: 993 loop : -1.53 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 446 TYR 0.047 0.001 TYR B 985 PHE 0.024 0.002 PHE H 32 TRP 0.028 0.002 TRP L 96 HIS 0.009 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33886) covalent geometry : angle 0.59811 / 0.30 (46164) SS BOND : bond 0.00568 / 0.24 ( 52) SS BOND : angle 0.94450 / 0.60 ( 104) hydrogen bonds : bond 0.04172 / 2.78 ( 1061) hydrogen bonds : angle 6.14141 / 4.17 ( 2934) link_BETA1-4 : bond 0.02688 / 1.41 ( 1) link_BETA1-4 : angle 1.63322 / 0.95 ( 3) link_NAG-ASN : bond 0.00418 / 0.29 ( 23) link_NAG-ASN : angle 3.88291 / 2.33 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 459 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.3704 (OUTLIER) cc_final: 0.3250 (pp) REVERT: A 103 PHE cc_start: 0.4545 (OUTLIER) cc_final: 0.4044 (m-80) REVERT: A 155 MET cc_start: 0.1395 (ppp) cc_final: 0.0383 (ttt) REVERT: A 266 TYR cc_start: 0.6089 (m-80) cc_final: 0.5849 (m-80) REVERT: A 360 LEU cc_start: 0.8501 (mm) cc_final: 0.8194 (mt) REVERT: A 560 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7242 (tt) REVERT: A 561 ASN cc_start: 0.7134 (t0) cc_final: 0.6804 (t0) REVERT: A 632 ILE cc_start: 0.9001 (mm) cc_final: 0.8711 (mt) REVERT: A 701 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7522 (mt) REVERT: A 735 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: A 835 PHE cc_start: 0.7653 (t80) cc_final: 0.7281 (t80) REVERT: A 1038 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 1126 ASN cc_start: 0.7204 (m-40) cc_final: 0.6823 (p0) REVERT: A 1205 MET cc_start: 0.3880 (mmp) cc_final: 0.3381 (mmt) REVERT: B 90 TYR cc_start: 0.6568 (m-10) cc_final: 0.6146 (m-10) REVERT: B 149 THR cc_start: 0.8148 (p) cc_final: 0.7880 (p) REVERT: B 155 MET cc_start: 0.7987 (mmt) cc_final: 0.7697 (mmt) REVERT: B 174 TRP cc_start: 0.4841 (p-90) cc_final: 0.4431 (p-90) REVERT: B 240 LEU cc_start: 0.7449 (tp) cc_final: 0.7241 (mt) REVERT: B 573 LEU cc_start: 0.2639 (OUTLIER) cc_final: 0.2262 (mp) REVERT: B 861 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7737 (mm) REVERT: B 1168 ARG cc_start: 0.3835 (ppt170) cc_final: 0.2010 (ttp80) REVERT: B 1172 PRO cc_start: 0.6998 (Cg_endo) cc_final: 0.6599 (Cg_exo) REVERT: C 213 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 301 THR cc_start: 0.8799 (m) cc_final: 0.8265 (p) REVERT: C 393 ILE cc_start: 0.7593 (mt) cc_final: 0.7391 (mt) REVERT: C 1008 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.4628 (t80) REVERT: C 1121 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7259 (mt) REVERT: C 1205 MET cc_start: 0.1397 (tpt) cc_final: -0.0039 (mmm) REVERT: I 77 HIS cc_start: 0.5761 (p90) cc_final: 0.5453 (p90) REVERT: M 35 TRP cc_start: 0.7109 (m100) cc_final: 0.6611 (m100) outliers start: 138 outliers final: 84 residues processed: 562 average time/residue: 0.1984 time to fit residues: 189.6546 Evaluate side-chains 471 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 377 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 760 SER Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1006 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 95 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 242 optimal weight: 0.0370 chunk 191 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 333 optimal weight: 0.2980 chunk 304 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 415 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 605 ASN A 821 ASN A1122 ASN B 100 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 954 GLN B 984 GLN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 204 GLN C 234 HIS C 265 GLN C 364 HIS C1001 GLN C1059 GLN C1122 ASN C1135 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN N 6 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.185876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.153466 restraints weight = 57242.465| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.56 r_work: 0.3681 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 33962 Z= 0.176 Angle : 0.650 22.714 46340 Z= 0.328 Chirality : 0.045 0.237 5259 Planarity : 0.004 0.054 5897 Dihedral : 5.017 58.591 5079 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 4.92 % Allowed : 15.78 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 4183 helix: 1.03 (0.20), residues: 739 sheet: -0.23 (0.16), residues: 989 loop : -1.63 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 446 TYR 0.032 0.002 TYR C 90 PHE 0.022 0.002 PHE B1051 TRP 0.025 0.002 TRP J 47 HIS 0.007 0.002 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (33886) covalent geometry : angle 0.63872 / 0.33 (46164) SS BOND : bond 0.00499 / 0.26 ( 52) SS BOND : angle 1.11376 / 0.71 ( 104) hydrogen bonds : bond 0.03689 / 2.42 ( 1061) hydrogen bonds : angle 5.68668 / 3.88 ( 2934) link_BETA1-4 : bond 0.00498 / 0.26 ( 1) link_BETA1-4 : angle 1.19686 / 0.67 ( 3) link_NAG-ASN : bond 0.00715 / 0.39 ( 23) link_NAG-ASN : angle 2.92059 / 1.95 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 432 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3458 (pp) REVERT: A 103 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.4242 (m-80) REVERT: A 155 MET cc_start: 0.1542 (ppp) cc_final: 0.0532 (ttt) REVERT: A 199 TYR cc_start: 0.5555 (m-80) cc_final: 0.5344 (m-10) REVERT: A 360 LEU cc_start: 0.8690 (mm) cc_final: 0.8332 (mt) REVERT: A 560 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7403 (tt) REVERT: A 632 ILE cc_start: 0.8976 (mm) cc_final: 0.8726 (mt) REVERT: A 835 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 1038 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 1205 MET cc_start: 0.5615 (mmp) cc_final: 0.4964 (mmt) REVERT: B 90 TYR cc_start: 0.7228 (m-10) cc_final: 0.6938 (m-10) REVERT: B 287 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 330 ASP cc_start: 0.5230 (OUTLIER) cc_final: 0.4704 (t70) REVERT: B 573 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2314 (mp) REVERT: B 656 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.5969 (mm) REVERT: B 1013 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6205 (mm) REVERT: B 1168 ARG cc_start: 0.4813 (ppt170) cc_final: 0.2882 (ttm-80) REVERT: B 1178 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6031 (pt) REVERT: C 26 ASN cc_start: 0.4751 (m110) cc_final: 0.3891 (m110) REVERT: C 59 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8191 (p) REVERT: C 301 THR cc_start: 0.8987 (m) cc_final: 0.8552 (p) REVERT: C 632 ILE cc_start: 0.8679 (mm) cc_final: 0.8338 (mt) REVERT: C 677 VAL cc_start: 0.8611 (p) cc_final: 0.8402 (p) REVERT: C 744 ILE cc_start: 0.8503 (mm) cc_final: 0.8230 (mm) REVERT: C 862 MET cc_start: 0.8461 (mmm) cc_final: 0.8183 (mmm) REVERT: C 1121 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7826 (mt) REVERT: C 1205 MET cc_start: 0.2301 (tpt) cc_final: 0.0897 (mmm) REVERT: J 96 THR cc_start: 0.6614 (p) cc_final: 0.6098 (p) REVERT: J 100 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5775 (mt-10) REVERT: J 105 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6876 (pp30) REVERT: M 35 TRP cc_start: 0.7392 (m100) cc_final: 0.6852 (m100) REVERT: M 95 ASN cc_start: 0.7735 (t0) cc_final: 0.7530 (t0) REVERT: N 85 ASP cc_start: 0.7374 (p0) cc_final: 0.6144 (p0) REVERT: N 87 TYR cc_start: 0.7297 (m-80) cc_final: 0.6727 (m-80) outliers start: 183 outliers final: 110 residues processed: 553 average time/residue: 0.1987 time to fit residues: 187.5067 Evaluate side-chains 491 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 368 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 760 SER Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 0 optimal weight: 10.9990 chunk 345 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 169 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 400 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 881 ASN A1041 ASN A1122 ASN A1126 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 GLN B 591 ASN ** B 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 364 HIS C 694 ASN C1006 ASN C1059 GLN C1122 ASN C1135 GLN I 77 HIS ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 95AASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131578 restraints weight = 55837.489| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.92 r_work: 0.3365 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33962 Z= 0.219 Angle : 0.704 22.251 46340 Z= 0.355 Chirality : 0.048 0.410 5259 Planarity : 0.005 0.074 5897 Dihedral : 5.111 59.372 5073 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.16 % Allowed : 16.64 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4183 helix: 0.78 (0.20), residues: 740 sheet: -0.32 (0.16), residues: 1009 loop : -1.65 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1105 TYR 0.033 0.002 TYR J 50 PHE 0.026 0.002 PHE A 222 TRP 0.040 0.002 TRP J 103 HIS 0.011 0.002 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (33886) covalent geometry : angle 0.68116 / 0.35 (46164) SS BOND : bond 0.00562 / 0.42 ( 52) SS BOND : angle 1.48512 / 1.09 ( 104) hydrogen bonds : bond 0.03588 / 2.35 ( 1061) hydrogen bonds : angle 5.69526 / 3.90 ( 2934) link_BETA1-4 : bond 0.00216 / 0.11 ( 1) link_BETA1-4 : angle 1.04590 / 0.57 ( 3) link_NAG-ASN : bond 0.01202 / 0.81 ( 23) link_NAG-ASN : angle 4.37538 / 2.57 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 407 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.4240 (OUTLIER) cc_final: 0.3262 (pp) REVERT: A 155 MET cc_start: 0.2105 (ppp) cc_final: 0.1006 (ttm) REVERT: A 360 LEU cc_start: 0.8824 (mm) cc_final: 0.8447 (mt) REVERT: A 560 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7382 (tt) REVERT: A 577 PHE cc_start: 0.7872 (p90) cc_final: 0.7623 (p90) REVERT: A 632 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 835 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7057 (t80) REVERT: A 870 ASN cc_start: 0.6710 (p0) cc_final: 0.6277 (p0) REVERT: A 884 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6889 (t80) REVERT: A 1041 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 1082 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8680 (mp) REVERT: B 330 ASP cc_start: 0.5305 (OUTLIER) cc_final: 0.4771 (t70) REVERT: B 573 LEU cc_start: 0.2917 (OUTLIER) cc_final: 0.2410 (mp) REVERT: B 656 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6859 (mm) REVERT: B 861 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 1168 ARG cc_start: 0.5785 (ppt170) cc_final: 0.3664 (ttm-80) REVERT: B 1178 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7038 (pt) REVERT: C 403 LEU cc_start: 0.9038 (mm) cc_final: 0.8821 (mt) REVERT: C 521 LEU cc_start: 0.8505 (mm) cc_final: 0.8222 (mm) REVERT: C 523 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6729 (p0) REVERT: C 632 ILE cc_start: 0.8847 (mm) cc_final: 0.8593 (mt) REVERT: C 862 MET cc_start: 0.8791 (mmm) cc_final: 0.8577 (mmm) REVERT: C 908 PHE cc_start: 0.7635 (m-10) cc_final: 0.7268 (m-80) REVERT: C 916 VAL cc_start: 0.8834 (m) cc_final: 0.8605 (p) REVERT: C 1060 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: C 1121 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 1156 VAL cc_start: 0.8424 (p) cc_final: 0.7904 (m) REVERT: C 1193 TYR cc_start: 0.6736 (t80) cc_final: 0.6528 (t80) REVERT: C 1205 MET cc_start: 0.3849 (tpt) cc_final: 0.2949 (mmm) REVERT: H 82 LEU cc_start: 0.3154 (mt) cc_final: 0.2621 (tt) REVERT: J 96 THR cc_start: 0.7157 (p) cc_final: 0.6464 (p) REVERT: J 105 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6622 (pp30) REVERT: M 54 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7605 (mtm110) REVERT: N 87 TYR cc_start: 0.7526 (m-80) cc_final: 0.7164 (m-80) REVERT: N 95 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7907 (t0) outliers start: 192 outliers final: 108 residues processed: 543 average time/residue: 0.1924 time to fit residues: 180.5078 Evaluate side-chains 471 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 346 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1083 THR Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 1006 ASN Chi-restraints excluded: chain C residue 1016 GLN Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 95 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 881 ASN A1041 ASN A1122 ASN A1126 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 826 HIS B 954 GLN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN C 353 ASN C 402 GLN C1006 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 95AASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135346 restraints weight = 55255.820| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.57 r_work: 0.3466 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33962 Z= 0.118 Angle : 0.574 14.532 46340 Z= 0.290 Chirality : 0.044 0.336 5259 Planarity : 0.004 0.058 5897 Dihedral : 4.662 53.989 5067 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.82 % Allowed : 18.61 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4183 helix: 0.94 (0.20), residues: 743 sheet: -0.24 (0.16), residues: 991 loop : -1.56 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 61 TYR 0.020 0.001 TYR I 52 PHE 0.025 0.001 PHE A 94 TRP 0.020 0.001 TRP J 47 HIS 0.007 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33886) covalent geometry : angle 0.56097 / 0.29 (46164) SS BOND : bond 0.00321 / 0.25 ( 52) SS BOND : angle 1.24554 / 0.95 ( 104) hydrogen bonds : bond 0.03057 / 2.00 ( 1061) hydrogen bonds : angle 5.40660 / 3.71 ( 2934) link_BETA1-4 : bond 0.00341 / 0.18 ( 1) link_BETA1-4 : angle 0.88896 / 0.49 ( 3) link_NAG-ASN : bond 0.00555 / 0.40 ( 23) link_NAG-ASN : angle 2.84152 / 1.64 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 370 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3329 (pp) REVERT: A 155 MET cc_start: 0.2086 (ppp) cc_final: 0.1043 (ttm) REVERT: A 360 LEU cc_start: 0.8765 (mm) cc_final: 0.8398 (mt) REVERT: A 560 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7346 (tt) REVERT: A 577 PHE cc_start: 0.7869 (p90) cc_final: 0.7636 (p90) REVERT: A 632 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 835 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 870 ASN cc_start: 0.6718 (p0) cc_final: 0.6307 (p0) REVERT: A 884 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7284 (t80) REVERT: A 1002 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7867 (mmtm) REVERT: A 1041 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (t0) REVERT: A 1082 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (mt) REVERT: B 330 ASP cc_start: 0.5072 (OUTLIER) cc_final: 0.4576 (t70) REVERT: B 573 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2415 (mp) REVERT: B 656 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6697 (mm) REVERT: B 1168 ARG cc_start: 0.5696 (ppt170) cc_final: 0.3836 (ttm-80) REVERT: B 1178 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6792 (pt) REVERT: C 213 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7626 (t80) REVERT: C 280 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9133 (m) REVERT: C 351 ASN cc_start: 0.7925 (t0) cc_final: 0.7671 (t0) REVERT: C 403 LEU cc_start: 0.8907 (mm) cc_final: 0.8549 (mt) REVERT: C 464 ASP cc_start: 0.7181 (m-30) cc_final: 0.6868 (m-30) REVERT: C 632 ILE cc_start: 0.8785 (mm) cc_final: 0.8541 (mt) REVERT: C 763 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: C 1060 GLU cc_start: 0.6796 (pt0) cc_final: 0.6586 (tt0) REVERT: C 1205 MET cc_start: 0.3848 (tpt) cc_final: 0.3333 (mmm) REVERT: I 47 TRP cc_start: 0.7641 (t60) cc_final: 0.7351 (t60) REVERT: N 85 ASP cc_start: 0.7857 (p0) cc_final: 0.7354 (p0) REVERT: N 87 TYR cc_start: 0.7397 (m-80) cc_final: 0.7193 (m-80) REVERT: N 95 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8127 (t0) outliers start: 142 outliers final: 93 residues processed: 473 average time/residue: 0.1905 time to fit residues: 156.1584 Evaluate side-chains 440 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 333 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain N residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 150 optimal weight: 0.0980 chunk 396 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 293 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 863 GLN A1034 ASN A1126 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 998 ASN C 160 HIS C 364 HIS C1122 ASN C1126 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95AASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123359 restraints weight = 54885.535| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.07 r_work: 0.3334 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 33962 Z= 0.186 Angle : 0.610 13.392 46340 Z= 0.311 Chirality : 0.046 0.353 5259 Planarity : 0.004 0.052 5897 Dihedral : 4.835 53.782 5067 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 4.65 % Allowed : 18.66 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4183 helix: 0.81 (0.20), residues: 743 sheet: -0.29 (0.17), residues: 968 loop : -1.56 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 61 TYR 0.021 0.002 TYR B 236 PHE 0.029 0.002 PHE A 209 TRP 0.017 0.001 TRP J 47 HIS 0.008 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (33886) covalent geometry : angle 0.59893 / 0.31 (46164) SS BOND : bond 0.00357 / 0.24 ( 52) SS BOND : angle 1.27565 / 0.92 ( 104) hydrogen bonds : bond 0.03158 / 2.06 ( 1061) hydrogen bonds : angle 5.39935 / 3.70 ( 2934) link_BETA1-4 : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : angle 1.08544 / 0.60 ( 3) link_NAG-ASN : bond 0.00366 / 0.27 ( 23) link_NAG-ASN : angle 2.70951 / 1.62 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 360 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.2210 (ppp) cc_final: 0.1257 (ttm) REVERT: A 360 LEU cc_start: 0.8876 (mm) cc_final: 0.8483 (mt) REVERT: A 560 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7377 (tt) REVERT: A 632 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (mt) REVERT: A 785 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.6768 (mp) REVERT: A 835 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7108 (t80) REVERT: A 870 ASN cc_start: 0.7086 (p0) cc_final: 0.6691 (p0) REVERT: A 884 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 1082 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 1162 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.6456 (pp) REVERT: B 54 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8003 (mtm-85) REVERT: B 330 ASP cc_start: 0.4846 (OUTLIER) cc_final: 0.4425 (t70) REVERT: B 573 LEU cc_start: 0.3109 (OUTLIER) cc_final: 0.2701 (mp) REVERT: B 649 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: B 656 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7213 (mm) REVERT: B 1168 ARG cc_start: 0.5929 (ppt170) cc_final: 0.4095 (ttp80) REVERT: C 213 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7747 (t80) REVERT: C 280 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9167 (m) REVERT: C 351 ASN cc_start: 0.8174 (t0) cc_final: 0.7899 (t0) REVERT: C 464 ASP cc_start: 0.7380 (m-30) cc_final: 0.7070 (m-30) REVERT: C 528 TYR cc_start: 0.7238 (m-80) cc_final: 0.6916 (m-80) REVERT: C 632 ILE cc_start: 0.8814 (mm) cc_final: 0.8581 (mt) REVERT: C 908 PHE cc_start: 0.7860 (m-80) cc_final: 0.7621 (m-80) REVERT: C 1003 LEU cc_start: 0.8523 (tt) cc_final: 0.7612 (mp) REVERT: C 1121 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8586 (mt) REVERT: H 4 LEU cc_start: -0.0122 (tp) cc_final: -0.0359 (tt) REVERT: H 82 LEU cc_start: 0.2274 (mt) cc_final: 0.1679 (tt) REVERT: J 53 TYR cc_start: 0.8023 (p90) cc_final: 0.7808 (p90) REVERT: J 96 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.6540 (p) REVERT: J 100 GLU cc_start: 0.6585 (mt-10) cc_final: 0.5965 (mt-10) REVERT: N 85 ASP cc_start: 0.7899 (p0) cc_final: 0.6419 (p0) REVERT: N 87 TYR cc_start: 0.7414 (m-80) cc_final: 0.6850 (m-80) outliers start: 173 outliers final: 114 residues processed: 480 average time/residue: 0.1912 time to fit residues: 158.8763 Evaluate side-chains 462 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 332 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 3 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 354 optimal weight: 30.0000 chunk 400 optimal weight: 9.9990 chunk 270 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 357 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A1045 GLN A1071 GLN A1126 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1006 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127896 restraints weight = 54933.445| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.63 r_work: 0.3360 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33962 Z= 0.136 Angle : 0.575 15.428 46340 Z= 0.292 Chirality : 0.044 0.333 5259 Planarity : 0.004 0.047 5897 Dihedral : 4.706 52.940 5065 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.01 % Allowed : 19.31 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4183 helix: 0.99 (0.20), residues: 738 sheet: -0.24 (0.16), residues: 986 loop : -1.48 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 61 TYR 0.028 0.002 TYR C 84 PHE 0.025 0.001 PHE A 94 TRP 0.015 0.001 TRP I 47 HIS 0.008 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (33886) covalent geometry : angle 0.56573 / 0.29 (46164) SS BOND : bond 0.00320 / 0.19 ( 52) SS BOND : angle 1.05835 / 0.74 ( 104) hydrogen bonds : bond 0.02940 / 1.91 ( 1061) hydrogen bonds : angle 5.24238 / 3.58 ( 2934) link_BETA1-4 : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : angle 1.00514 / 0.56 ( 3) link_NAG-ASN : bond 0.00338 / 0.25 ( 23) link_NAG-ASN : angle 2.42773 / 1.47 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 341 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8001 (tp) cc_final: 0.7784 (tp) REVERT: A 155 MET cc_start: 0.2219 (ppp) cc_final: 0.1350 (ttm) REVERT: A 296 SER cc_start: 0.8687 (t) cc_final: 0.8459 (p) REVERT: A 360 LEU cc_start: 0.8831 (mm) cc_final: 0.8450 (mt) REVERT: A 560 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7435 (tt) REVERT: A 577 PHE cc_start: 0.8549 (p90) cc_final: 0.8059 (p90) REVERT: A 632 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (mt) REVERT: A 884 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7735 (t80) REVERT: A 1162 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6519 (pp) REVERT: B 54 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7997 (mtm-85) REVERT: B 215 ASP cc_start: 0.7282 (p0) cc_final: 0.7077 (p0) REVERT: B 330 ASP cc_start: 0.5172 (OUTLIER) cc_final: 0.4665 (t70) REVERT: B 387 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6764 (m) REVERT: B 573 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.2590 (mp) REVERT: B 656 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 1168 ARG cc_start: 0.5983 (ppt170) cc_final: 0.4386 (ttm-80) REVERT: B 1205 MET cc_start: 0.7499 (mmt) cc_final: 0.6874 (mtt) REVERT: C 213 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7651 (t80) REVERT: C 280 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9158 (m) REVERT: C 351 ASN cc_start: 0.8168 (t0) cc_final: 0.7916 (t0) REVERT: C 464 ASP cc_start: 0.7311 (m-30) cc_final: 0.7059 (m-30) REVERT: C 528 TYR cc_start: 0.6955 (m-80) cc_final: 0.6606 (m-80) REVERT: C 632 ILE cc_start: 0.8780 (mm) cc_final: 0.8558 (mt) REVERT: C 673 TYR cc_start: 0.7567 (t80) cc_final: 0.7323 (t80) REVERT: C 1060 GLU cc_start: 0.7695 (tt0) cc_final: 0.7323 (tm-30) REVERT: C 1121 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8636 (mt) REVERT: H 4 LEU cc_start: -0.0398 (tp) cc_final: -0.0608 (tt) REVERT: H 82 LEU cc_start: 0.2659 (mt) cc_final: 0.1999 (tt) REVERT: J 96 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6640 (p) REVERT: J 100 GLU cc_start: 0.6547 (mt-10) cc_final: 0.5953 (mt-10) REVERT: N 85 ASP cc_start: 0.8125 (p0) cc_final: 0.6632 (p0) REVERT: N 87 TYR cc_start: 0.7433 (m-80) cc_final: 0.6857 (m-80) REVERT: N 102 THR cc_start: 0.8311 (m) cc_final: 0.7720 (p) outliers start: 149 outliers final: 107 residues processed: 444 average time/residue: 0.1812 time to fit residues: 139.7036 Evaluate side-chains 439 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 319 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1006 ASN Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 363 optimal weight: 30.0000 chunk 411 optimal weight: 0.4980 chunk 243 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 410 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1041 ASN C1049 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122715 restraints weight = 54739.602| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.74 r_work: 0.3306 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33962 Z= 0.147 Angle : 0.584 14.322 46340 Z= 0.296 Chirality : 0.045 0.335 5259 Planarity : 0.004 0.048 5897 Dihedral : 4.738 53.716 5065 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.01 % Allowed : 19.33 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 4183 helix: 0.88 (0.20), residues: 748 sheet: -0.27 (0.16), residues: 1003 loop : -1.45 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1105 TYR 0.029 0.002 TYR A 213 PHE 0.026 0.002 PHE A 94 TRP 0.013 0.001 TRP J 47 HIS 0.009 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (33886) covalent geometry : angle 0.57566 / 0.29 (46164) SS BOND : bond 0.00279 / 0.19 ( 52) SS BOND : angle 1.12577 / 0.82 ( 104) hydrogen bonds : bond 0.03052 / 2.01 ( 1061) hydrogen bonds : angle 5.23326 / 3.58 ( 2934) link_BETA1-4 : bond 0.00457 / 0.24 ( 1) link_BETA1-4 : angle 0.73586 / 0.40 ( 3) link_NAG-ASN : bond 0.00308 / 0.23 ( 23) link_NAG-ASN : angle 2.31203 / 1.41 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 346 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.2289 (ppp) cc_final: 0.1423 (ttm) REVERT: A 296 SER cc_start: 0.8734 (t) cc_final: 0.8477 (p) REVERT: A 360 LEU cc_start: 0.8849 (mm) cc_final: 0.8451 (mt) REVERT: A 560 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7419 (tt) REVERT: A 632 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 870 ASN cc_start: 0.7162 (p0) cc_final: 0.6698 (p0) REVERT: A 884 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 54 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7963 (mtm-85) REVERT: B 215 ASP cc_start: 0.7371 (p0) cc_final: 0.7163 (p0) REVERT: B 330 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4678 (t70) REVERT: B 573 LEU cc_start: 0.3067 (OUTLIER) cc_final: 0.2603 (mp) REVERT: B 656 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7519 (mm) REVERT: B 1059 GLN cc_start: 0.6566 (pt0) cc_final: 0.6328 (pt0) REVERT: B 1168 ARG cc_start: 0.6177 (ppt170) cc_final: 0.4507 (ttp-170) REVERT: B 1205 MET cc_start: 0.7954 (mmt) cc_final: 0.7350 (mtt) REVERT: C 280 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9166 (m) REVERT: C 464 ASP cc_start: 0.7351 (m-30) cc_final: 0.7094 (m-30) REVERT: C 521 LEU cc_start: 0.8425 (mm) cc_final: 0.8177 (mm) REVERT: C 528 TYR cc_start: 0.6987 (m-80) cc_final: 0.6663 (m-80) REVERT: C 632 ILE cc_start: 0.8798 (mm) cc_final: 0.8577 (mt) REVERT: C 673 TYR cc_start: 0.7598 (t80) cc_final: 0.7395 (t80) REVERT: C 1184 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7869 (t-100) REVERT: H 82 LEU cc_start: 0.2622 (mt) cc_final: 0.1972 (tt) REVERT: J 53 TYR cc_start: 0.7910 (p90) cc_final: 0.7684 (p90) REVERT: J 96 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.6594 (p) REVERT: J 100 GLU cc_start: 0.6461 (mt-10) cc_final: 0.5795 (mt-10) REVERT: N 85 ASP cc_start: 0.8018 (p0) cc_final: 0.6730 (p0) REVERT: N 87 TYR cc_start: 0.7365 (m-80) cc_final: 0.6890 (m-80) outliers start: 149 outliers final: 117 residues processed: 455 average time/residue: 0.1807 time to fit residues: 142.0701 Evaluate side-chains 449 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 322 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 58 optimal weight: 6.9990 chunk 377 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 196 optimal weight: 0.4980 chunk 407 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 331 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 988 ASN A1086 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 ASN B1135 GLN C 954 GLN C1006 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122523 restraints weight = 54416.489| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.76 r_work: 0.3325 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33962 Z= 0.116 Angle : 0.572 15.014 46340 Z= 0.289 Chirality : 0.044 0.278 5259 Planarity : 0.004 0.048 5897 Dihedral : 4.630 53.110 5065 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.28 % Allowed : 20.46 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % 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: -0.96 (0.13), residues: 4183 helix: 1.06 (0.20), residues: 745 sheet: -0.23 (0.16), residues: 1011 loop : -1.41 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 61 TYR 0.026 0.001 TYR I 52 PHE 0.028 0.001 PHE B 884 TRP 0.020 0.001 TRP A 575 HIS 0.009 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33886) covalent geometry : angle 0.56529 / 0.29 (46164) SS BOND : bond 0.00346 / 0.25 ( 52) SS BOND : angle 1.00063 / 0.73 ( 104) hydrogen bonds : bond 0.02820 / 1.84 ( 1061) hydrogen bonds : angle 5.12350 / 3.49 ( 2934) link_BETA1-4 : bond 0.00249 / 0.13 ( 1) link_BETA1-4 : angle 0.78049 / 0.43 ( 3) link_NAG-ASN : bond 0.00301 / 0.22 ( 23) link_NAG-ASN : angle 2.17298 / 1.33 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 350 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.2258 (ppp) cc_final: 0.1455 (ttm) REVERT: A 296 SER cc_start: 0.8790 (t) cc_final: 0.8560 (p) REVERT: A 360 LEU cc_start: 0.8808 (mm) cc_final: 0.8439 (mt) REVERT: A 560 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 632 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 884 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 215 ASP cc_start: 0.7276 (p0) cc_final: 0.7007 (p0) REVERT: B 330 ASP cc_start: 0.5075 (OUTLIER) cc_final: 0.4593 (t70) REVERT: B 387 THR cc_start: 0.6788 (OUTLIER) cc_final: 0.6543 (m) REVERT: B 573 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2563 (mp) REVERT: B 656 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7545 (mm) REVERT: B 1059 GLN cc_start: 0.6452 (pt0) cc_final: 0.6200 (pt0) REVERT: B 1168 ARG cc_start: 0.6136 (ppt170) cc_final: 0.4783 (ttm-80) REVERT: B 1205 MET cc_start: 0.7660 (mmt) cc_final: 0.7237 (mtt) REVERT: C 280 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9128 (m) REVERT: C 464 ASP cc_start: 0.7301 (m-30) cc_final: 0.7076 (m-30) REVERT: C 521 LEU cc_start: 0.8290 (mm) cc_final: 0.8074 (mm) REVERT: C 528 TYR cc_start: 0.6928 (m-80) cc_final: 0.6312 (m-80) REVERT: C 632 ILE cc_start: 0.8787 (mm) cc_final: 0.8557 (mt) REVERT: C 1184 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7684 (t-100) REVERT: H 82 LEU cc_start: 0.2519 (OUTLIER) cc_final: 0.1918 (tt) REVERT: I 47 TRP cc_start: 0.7645 (t60) cc_final: 0.7192 (t60) REVERT: J 53 TYR cc_start: 0.7837 (p90) cc_final: 0.7579 (p90) REVERT: J 96 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6675 (p) REVERT: N 85 ASP cc_start: 0.7994 (p0) cc_final: 0.6723 (p0) REVERT: N 87 TYR cc_start: 0.7294 (m-80) cc_final: 0.6925 (m-80) outliers start: 122 outliers final: 97 residues processed: 438 average time/residue: 0.1782 time to fit residues: 135.0999 Evaluate side-chains 431 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 323 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 308 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 314 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 321 optimal weight: 0.9980 chunk 241 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 988 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123944 restraints weight = 54950.656| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.59 r_work: 0.3307 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33962 Z= 0.136 Angle : 0.594 17.332 46340 Z= 0.297 Chirality : 0.044 0.287 5259 Planarity : 0.004 0.048 5897 Dihedral : 4.654 53.912 5065 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.33 % Allowed : 20.60 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % 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: -0.94 (0.13), residues: 4183 helix: 1.04 (0.20), residues: 752 sheet: -0.20 (0.16), residues: 1011 loop : -1.39 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 61 TYR 0.029 0.001 TYR B 649 PHE 0.025 0.001 PHE B 884 TRP 0.014 0.001 TRP M 35 HIS 0.008 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (33886) covalent geometry : angle 0.57883 / 0.29 (46164) SS BOND : bond 0.00272 / 0.18 ( 52) SS BOND : angle 1.18692 / 0.92 ( 104) hydrogen bonds : bond 0.02850 / 1.86 ( 1061) hydrogen bonds : angle 5.10825 / 3.49 ( 2934) link_BETA1-4 : bond 0.00308 / 0.16 ( 1) link_BETA1-4 : angle 1.11777 / 0.60 ( 3) link_NAG-ASN : bond 0.00502 / 0.37 ( 23) link_NAG-ASN : angle 3.29195 / 1.83 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8366 Ramachandran restraints generated. 4183 Oldfield, 0 Emsley, 4183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 332 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.2699 (m-80) cc_final: 0.1980 (p90) REVERT: A 155 MET cc_start: 0.2494 (ppp) cc_final: 0.1663 (ttm) REVERT: A 296 SER cc_start: 0.8872 (t) cc_final: 0.8643 (p) REVERT: A 360 LEU cc_start: 0.8851 (mm) cc_final: 0.8475 (mt) REVERT: A 560 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7413 (tt) REVERT: A 884 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 54 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: B 215 ASP cc_start: 0.7518 (p0) cc_final: 0.7294 (p0) REVERT: B 330 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4756 (t70) REVERT: B 387 THR cc_start: 0.6948 (OUTLIER) cc_final: 0.6655 (m) REVERT: B 573 LEU cc_start: 0.2875 (OUTLIER) cc_final: 0.2423 (mp) REVERT: B 1168 ARG cc_start: 0.6450 (ppt170) cc_final: 0.4999 (ttm-80) REVERT: B 1185 MET cc_start: 0.8743 (tpp) cc_final: 0.8413 (mtp) REVERT: B 1205 MET cc_start: 0.8128 (mmt) cc_final: 0.7510 (mtt) REVERT: C 280 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9144 (m) REVERT: C 464 ASP cc_start: 0.7535 (m-30) cc_final: 0.7295 (m-30) REVERT: C 528 TYR cc_start: 0.6994 (m-80) cc_final: 0.6352 (m-80) REVERT: C 632 ILE cc_start: 0.8869 (mm) cc_final: 0.8654 (mt) REVERT: C 1038 GLN cc_start: 0.8461 (tt0) cc_final: 0.8223 (tm-30) REVERT: C 1184 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7759 (t-100) REVERT: H 82 LEU cc_start: 0.2595 (OUTLIER) cc_final: 0.2011 (tt) REVERT: J 33 TYR cc_start: 0.8419 (m-80) cc_final: 0.8180 (m-80) REVERT: J 53 TYR cc_start: 0.7977 (p90) cc_final: 0.7678 (p90) REVERT: J 96 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.6801 (p) REVERT: N 85 ASP cc_start: 0.8112 (p0) cc_final: 0.6918 (p0) REVERT: N 87 TYR cc_start: 0.7452 (m-80) cc_final: 0.7045 (m-80) REVERT: N 102 THR cc_start: 0.8362 (m) cc_final: 0.7798 (p) outliers start: 124 outliers final: 103 residues processed: 424 average time/residue: 0.1860 time to fit residues: 135.7917 Evaluate side-chains 429 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 316 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 284 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 343 optimal weight: 0.1980 chunk 296 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 847 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS C1049 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116193 restraints weight = 54501.449| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.53 r_work: 0.3237 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 33962 Z= 0.232 Angle : 0.688 22.921 46340 Z= 0.348 Chirality : 0.048 0.478 5259 Planarity : 0.004 0.047 5897 Dihedral : 5.137 56.064 5065 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.63 % Allowed : 20.25 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4183 helix: 0.77 (0.19), residues: 752 sheet: -0.29 (0.16), residues: 1041 loop : -1.46 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 361 TYR 0.034 0.002 TYR B 649 PHE 0.027 0.002 PHE B 884 TRP 0.023 0.002 TRP A1184 HIS 0.008 0.001 HIS C1145 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (33886) covalent geometry : angle 0.67293 / 0.34 (46164) SS BOND : bond 0.00495 / 0.36 ( 52) SS BOND : angle 1.61601 / 1.20 ( 104) hydrogen bonds : bond 0.03315 / 2.17 ( 1061) hydrogen bonds : angle 5.37843 / 3.67 ( 2934) link_BETA1-4 : bond 0.00052 / 0.03 ( 1) link_BETA1-4 : angle 1.12491 / 0.60 ( 3) link_NAG-ASN : bond 0.00611 / 0.45 ( 23) link_NAG-ASN : angle 3.36028 / 1.84 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8502.40 seconds wall clock time: 146 minutes 52.59 seconds (8812.59 seconds total)