Starting phenix.real_space_refine on Tue Apr 7 12:28:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yok_73260/04_2026/9yok_73260.map" } resolution = 3.56 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= 0.001 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 112 5.16 5 C 17224 2.51 5 N 4454 2.21 5 O 5277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27067 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 7720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7720 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 49, 'TRANS': 939} Chain breaks: 10 Chain: "C" Number of atoms: 7746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7746 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 12 Chain: "D" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1664 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain breaks: 2 Chain: "E" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1563 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" 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: "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: "L" 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: "M" 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: "N" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 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 Time building chain proxies: 6.22, per 1000 atoms: 0.23 Number of scatterers: 27067 At special positions: 0 Unit cell: (140.935, 158.552, 201.336, 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 112 16.00 O 5277 8.00 N 4454 7.00 C 17224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A 801 " " NAG B1301 " - " ASN B1098 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 331 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN B1134 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN C 709 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 234 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 58 sheets defined 22.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.560A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.813A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.515A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.128A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.703A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.902A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.792A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.948A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.603A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.108A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 942 removed outlier: 4.546A pdb=" N ALA B 942 " --> pdb=" O LEU B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.420A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.588A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.800A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.590A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.960A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.992A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.153A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.317A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.827A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.030A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.890A pdb=" N LEU D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.585A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.739A pdb=" N HIS E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.751A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.773A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.715A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.434A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.714A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.610A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.509A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.930A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.479A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.787A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.027A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.654A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.911A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.144A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.026A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.501A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 225 through 229 Processing sheet with id=AD8, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.577A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.900A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 396 through 400 Processing sheet with id=AE4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.116A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.978A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.966A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.393A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.924A pdb=" N ARG D 101 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 135 through 139 Processing sheet with id=AF6, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.552A pdb=" N SER D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 166 through 169 Processing sheet with id=AF8, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AF9, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AG1, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.146A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 92 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER E 98 " --> pdb=" O SER E 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.998A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.998A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 154 through 155 1014 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8590 1.34 - 1.46: 6370 1.46 - 1.58: 12556 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 27654 Sorted by residual: bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE A 670 " pdb=" CA ILE A 670 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE A 693 " pdb=" CA ILE A 693 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE A 664 " pdb=" CA ILE A 664 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.01e-02 9.80e+03 9.74e+00 bond pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.36e+00 ... (remaining 27649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 37024 2.16 - 4.31: 541 4.31 - 6.47: 38 6.47 - 8.63: 5 8.63 - 10.78: 5 Bond angle restraints: 37613 Sorted by residual: angle pdb=" C GLU A 96 " pdb=" CA GLU A 96 " pdb=" CB GLU A 96 " ideal model delta sigma weight residual 115.89 110.70 5.19 1.32e+00 5.74e-01 1.55e+01 angle pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " pdb=" CG GLU A 224 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N TYR D 113 " pdb=" CA TYR D 113 " pdb=" C TYR D 113 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.25e+01 angle pdb=" CA LEU C 276 " pdb=" C LEU C 276 " pdb=" O LEU C 276 " ideal model delta sigma weight residual 122.37 118.31 4.06 1.15e+00 7.56e-01 1.25e+01 angle pdb=" CA ASN C 121 " pdb=" C ASN C 121 " pdb=" O ASN C 121 " ideal model delta sigma weight residual 122.64 118.41 4.23 1.25e+00 6.40e-01 1.14e+01 ... (remaining 37608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14713 17.96 - 35.92: 1689 35.92 - 53.88: 441 53.88 - 71.84: 85 71.84 - 89.80: 48 Dihedral angle restraints: 16976 sinusoidal: 7073 harmonic: 9903 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.38 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 174.61 -81.61 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -6.34 -79.66 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 16973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4034 0.087 - 0.175: 346 0.175 - 0.262: 14 0.262 - 0.349: 1 0.349 - 0.436: 5 Chirality restraints: 4400 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.37e+02 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 4397 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.057 2.00e-02 2.50e+03 4.72e-02 2.79e+01 pdb=" C7 NAG A1307 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.055 2.00e-02 2.50e+03 4.50e-02 2.54e+01 pdb=" C7 NAG I 1 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.070 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 986 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 613 2.67 - 3.23: 25948 3.23 - 3.78: 42037 3.78 - 4.34: 54924 4.34 - 4.90: 91390 Nonbonded interactions: 214912 Sorted by model distance: nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 2.148 3.120 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.196 3.040 nonbonded pdb=" O SER A 967 " pdb=" OG SER A 967 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLN D 105 " pdb=" N VAL D 107 " model vdw 2.204 3.120 ... (remaining 214907 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 28 through 67 or resid 80 through 134 or resid 140 or resi \ d 157 through 159 or resid 170 through 171 or resid 187 through 212 or resid 217 \ through 241 or resid 263 through 265 or resid 267 through 471 or resid 489 thro \ ugh 496 or resid 503 through 620 or resid 641 through 1305)) selection = (chain 'B' and (resid 28 through 135 or resid 157 through 159 or resid 170 throu \ gh 171 or resid 187 through 471 or resid 489 through 496 or resid 503 through 82 \ 9 or resid 854 through 940 or resid 944 through 1074 or (resid 1075 and (name N \ or name CA or name C or name O or name CB )) or resid 1076 through 1305)) selection = (chain 'C' and (resid 28 through 67 or resid 80 through 134 or resid 140 or resi \ d 157 through 159 or resid 170 through 171 or resid 187 through 241 or resid 263 \ through 265 or resid 267 through 620 or resid 641 through 1074 or (resid 1075 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1076 through 13 \ 05)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = 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 group one per residue 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.680 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27733 Z= 0.210 Angle : 0.636 20.218 37809 Z= 0.333 Chirality : 0.048 0.436 4400 Planarity : 0.004 0.051 4801 Dihedral : 16.478 89.797 10473 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 0.71 % Allowed : 28.41 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3328 helix: 2.18 (0.21), residues: 654 sheet: -0.20 (0.18), residues: 794 loop : -1.49 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1014 TYR 0.022 0.001 TYR C 505 PHE 0.031 0.001 PHE C 392 TRP 0.013 0.001 TRP A 104 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00401 (27654) covalent geometry : angle 0.60456 (37613) SS BOND : bond 0.00235 ( 41) SS BOND : angle 0.99163 ( 82) hydrogen bonds : bond 0.14136 ( 989) hydrogen bonds : angle 6.79580 ( 2718) link_BETA1-4 : bond 0.01467 ( 10) link_BETA1-4 : angle 4.57004 ( 30) link_NAG-ASN : bond 0.00417 ( 28) link_NAG-ASN : angle 3.12700 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.026 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 64 TRP cc_start: 0.7334 (OUTLIER) cc_final: 0.6267 (t60) REVERT: A 817 PHE cc_start: 0.6441 (t80) cc_final: 0.6191 (t80) REVERT: B 201 PHE cc_start: 0.8807 (t80) cc_final: 0.8060 (t80) REVERT: B 571 ASP cc_start: 0.8633 (t0) cc_final: 0.8154 (t0) REVERT: B 740 MET cc_start: 0.8548 (tpt) cc_final: 0.8236 (tpt) REVERT: B 894 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 995 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8417 (mtp85) REVERT: B 1029 MET cc_start: 0.9308 (tpp) cc_final: 0.8792 (ttm) REVERT: C 113 LYS cc_start: 0.9425 (mmtm) cc_final: 0.9091 (mmmm) REVERT: C 276 LEU cc_start: 0.9070 (tp) cc_final: 0.8818 (tp) REVERT: C 335 LEU cc_start: 0.8359 (tt) cc_final: 0.7778 (mp) REVERT: C 368 LEU cc_start: 0.7670 (tt) cc_final: 0.7363 (mt) REVERT: C 756 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 1039 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8633 (ptm160) REVERT: D 27 ASP cc_start: 0.8408 (t0) cc_final: 0.7875 (m-30) REVERT: D 115 MET cc_start: 0.8849 (mmm) cc_final: 0.7940 (mmm) REVERT: D 158 LYS cc_start: 0.8394 (pttm) cc_final: 0.7581 (mtpt) REVERT: E 56 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.7881 (ttp80) REVERT: E 58 SER cc_start: 0.6820 (t) cc_final: 0.6430 (p) REVERT: E 81 GLN cc_start: 0.8737 (mp10) cc_final: 0.8280 (mp10) outliers start: 21 outliers final: 15 residues processed: 239 average time/residue: 0.1950 time to fit residues: 73.0510 Evaluate side-chains 190 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain D residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 448 ASN B 762 GLN B 978 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1106 GLN E 189 HIS E 195 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.117928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071267 restraints weight = 66763.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073845 restraints weight = 28431.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075592 restraints weight = 17347.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076485 restraints weight = 12933.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077340 restraints weight = 11059.398| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27733 Z= 0.118 Angle : 0.580 11.554 37809 Z= 0.286 Chirality : 0.045 0.427 4400 Planarity : 0.004 0.048 4801 Dihedral : 6.531 59.585 4472 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 3.74 % Allowed : 25.75 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3328 helix: 2.03 (0.21), residues: 674 sheet: -0.20 (0.18), residues: 814 loop : -1.47 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.025 0.001 TYR E 62 PHE 0.016 0.001 PHE A 817 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00263 (27654) covalent geometry : angle 0.55516 (37613) SS BOND : bond 0.00241 ( 41) SS BOND : angle 1.05679 ( 82) hydrogen bonds : bond 0.03937 ( 989) hydrogen bonds : angle 5.43722 ( 2718) link_BETA1-4 : bond 0.00836 ( 10) link_BETA1-4 : angle 3.23931 ( 30) link_NAG-ASN : bond 0.00433 ( 28) link_NAG-ASN : angle 2.94802 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 184 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7303 (p90) REVERT: A 988 GLU cc_start: 0.8493 (tp30) cc_final: 0.8124 (tm-30) REVERT: A 1086 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7816 (pttm) REVERT: B 201 PHE cc_start: 0.8903 (t80) cc_final: 0.8065 (t80) REVERT: B 303 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8874 (mt) REVERT: B 364 ASP cc_start: 0.8561 (t0) cc_final: 0.7988 (t70) REVERT: B 571 ASP cc_start: 0.8455 (t0) cc_final: 0.7948 (t0) REVERT: B 740 MET cc_start: 0.8421 (tpt) cc_final: 0.8176 (tpt) REVERT: B 995 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8403 (mtp85) REVERT: B 1029 MET cc_start: 0.9107 (tpp) cc_final: 0.8575 (ttm) REVERT: C 113 LYS cc_start: 0.9401 (mmtm) cc_final: 0.9179 (mmmm) REVERT: C 157 PHE cc_start: 0.5453 (m-80) cc_final: 0.5222 (m-80) REVERT: C 158 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7528 (mmm160) REVERT: C 335 LEU cc_start: 0.8475 (tt) cc_final: 0.7874 (mp) REVERT: C 378 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.5074 (mtmt) REVERT: C 756 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7933 (t80) REVERT: D 27 ASP cc_start: 0.8347 (t0) cc_final: 0.7835 (m-30) REVERT: D 115 MET cc_start: 0.8736 (mmm) cc_final: 0.8074 (mmm) REVERT: E 56 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8334 (ttp-170) REVERT: E 58 SER cc_start: 0.6625 (t) cc_final: 0.6225 (p) REVERT: E 190 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7068 (mmm160) outliers start: 111 outliers final: 60 residues processed: 277 average time/residue: 0.1797 time to fit residues: 80.2790 Evaluate side-chains 228 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 135 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 205 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 762 GLN C 30 ASN C 122 ASN C 280 ASN C1101 HIS E 185 GLN E 195 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.116199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069130 restraints weight = 67518.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071691 restraints weight = 29492.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073333 restraints weight = 18114.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074446 restraints weight = 13643.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074916 restraints weight = 11599.729| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27733 Z= 0.180 Angle : 0.589 11.689 37809 Z= 0.292 Chirality : 0.046 0.419 4400 Planarity : 0.004 0.050 4801 Dihedral : 6.499 56.851 4454 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 5.65 % Allowed : 24.00 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3328 helix: 1.96 (0.21), residues: 675 sheet: -0.16 (0.19), residues: 773 loop : -1.50 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.015 0.001 TYR C1067 PHE 0.030 0.001 PHE A 817 TRP 0.009 0.001 TRP E 186 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00415 (27654) covalent geometry : angle 0.56360 (37613) SS BOND : bond 0.00222 ( 41) SS BOND : angle 1.07005 ( 82) hydrogen bonds : bond 0.04046 ( 989) hydrogen bonds : angle 5.20263 ( 2718) link_BETA1-4 : bond 0.00717 ( 10) link_BETA1-4 : angle 3.31085 ( 30) link_NAG-ASN : bond 0.00389 ( 28) link_NAG-ASN : angle 2.98604 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 168 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7426 (p90) REVERT: A 562 PHE cc_start: 0.7780 (p90) cc_final: 0.7269 (p90) REVERT: A 988 GLU cc_start: 0.8489 (tp30) cc_final: 0.8187 (tm-30) REVERT: A 1086 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7856 (pttm) REVERT: B 201 PHE cc_start: 0.8818 (t80) cc_final: 0.8368 (t80) REVERT: B 303 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8893 (mt) REVERT: B 364 ASP cc_start: 0.8462 (t0) cc_final: 0.7812 (t0) REVERT: B 571 ASP cc_start: 0.8485 (t0) cc_final: 0.7946 (t0) REVERT: B 584 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8574 (tp) REVERT: B 988 GLU cc_start: 0.8999 (tp30) cc_final: 0.8356 (tp30) REVERT: B 995 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8426 (mtp85) REVERT: B 1029 MET cc_start: 0.9195 (tpp) cc_final: 0.8767 (ttm) REVERT: C 113 LYS cc_start: 0.9423 (mmtm) cc_final: 0.9127 (mmmm) REVERT: C 335 LEU cc_start: 0.8539 (tt) cc_final: 0.7949 (mp) REVERT: C 555 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7321 (p) REVERT: C 590 CYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6144 (m) REVERT: C 756 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8095 (t80) REVERT: D 27 ASP cc_start: 0.8338 (t0) cc_final: 0.7833 (m-30) REVERT: D 115 MET cc_start: 0.8782 (mmm) cc_final: 0.8050 (mmm) REVERT: E 34 TYR cc_start: 0.7716 (m-80) cc_final: 0.7495 (m-80) REVERT: E 56 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7853 (ttp80) REVERT: E 58 SER cc_start: 0.6717 (t) cc_final: 0.6363 (p) REVERT: E 190 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6957 (mmm160) outliers start: 168 outliers final: 106 residues processed: 320 average time/residue: 0.1702 time to fit residues: 89.0574 Evaluate side-chains 270 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 155 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 30 optimal weight: 0.9990 chunk 331 optimal weight: 8.9990 chunk 179 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 312 optimal weight: 30.0000 chunk 264 optimal weight: 0.0060 chunk 258 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 762 GLN C1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070115 restraints weight = 66962.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072726 restraints weight = 29190.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074417 restraints weight = 17845.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075561 restraints weight = 13410.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076161 restraints weight = 11335.228| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27733 Z= 0.130 Angle : 0.570 11.541 37809 Z= 0.281 Chirality : 0.045 0.426 4400 Planarity : 0.004 0.051 4801 Dihedral : 6.348 57.164 4450 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 4.98 % Allowed : 24.67 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3328 helix: 2.08 (0.21), residues: 667 sheet: -0.11 (0.19), residues: 773 loop : -1.47 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.016 0.001 TYR C1067 PHE 0.028 0.001 PHE A 817 TRP 0.008 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00300 (27654) covalent geometry : angle 0.54327 (37613) SS BOND : bond 0.00242 ( 41) SS BOND : angle 1.42712 ( 82) hydrogen bonds : bond 0.03735 ( 989) hydrogen bonds : angle 5.01712 ( 2718) link_BETA1-4 : bond 0.00820 ( 10) link_BETA1-4 : angle 3.20846 ( 30) link_NAG-ASN : bond 0.00398 ( 28) link_NAG-ASN : angle 2.92520 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 169 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7310 (t60) REVERT: A 158 ARG cc_start: -0.1136 (OUTLIER) cc_final: -0.4945 (ttt180) REVERT: A 318 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7363 (p90) REVERT: A 347 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.4483 (t80) REVERT: A 988 GLU cc_start: 0.8551 (tp30) cc_final: 0.8198 (tm-30) REVERT: A 1086 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7807 (pttm) REVERT: B 117 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7130 (mm) REVERT: B 201 PHE cc_start: 0.8683 (t80) cc_final: 0.8390 (t80) REVERT: B 303 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (mt) REVERT: B 364 ASP cc_start: 0.8555 (t0) cc_final: 0.7861 (t0) REVERT: B 571 ASP cc_start: 0.8492 (t0) cc_final: 0.8150 (t0) REVERT: B 584 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8517 (tp) REVERT: B 988 GLU cc_start: 0.9019 (tp30) cc_final: 0.8357 (tp30) REVERT: B 995 ARG cc_start: 0.8663 (tpp80) cc_final: 0.8460 (mtp85) REVERT: B 1029 MET cc_start: 0.9146 (tpp) cc_final: 0.8798 (ttm) REVERT: C 113 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9156 (mmmm) REVERT: C 158 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7623 (mmm160) REVERT: C 335 LEU cc_start: 0.8534 (tt) cc_final: 0.8018 (mp) REVERT: C 555 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7298 (p) REVERT: C 590 CYS cc_start: 0.6381 (OUTLIER) cc_final: 0.6118 (m) REVERT: C 756 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8070 (t80) REVERT: D 27 ASP cc_start: 0.8351 (t0) cc_final: 0.7830 (m-30) REVERT: D 115 MET cc_start: 0.8757 (mmm) cc_final: 0.8047 (mmm) REVERT: E 56 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: E 58 SER cc_start: 0.6652 (t) cc_final: 0.6245 (p) REVERT: E 190 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6895 (mmm160) outliers start: 148 outliers final: 99 residues processed: 299 average time/residue: 0.1679 time to fit residues: 82.6607 Evaluate side-chains 268 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 155 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 334 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 243 optimal weight: 0.0470 chunk 196 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 295 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 211 ASN C1083 HIS E 185 GLN E 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.117817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071307 restraints weight = 66807.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073857 restraints weight = 28877.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075553 restraints weight = 17540.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076698 restraints weight = 13126.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077167 restraints weight = 11107.704| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27733 Z= 0.109 Angle : 0.555 11.301 37809 Z= 0.271 Chirality : 0.045 0.420 4400 Planarity : 0.003 0.051 4801 Dihedral : 6.183 58.220 4448 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 4.85 % Allowed : 24.74 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3328 helix: 2.14 (0.21), residues: 663 sheet: -0.10 (0.19), residues: 790 loop : -1.43 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.021 0.001 TYR E 62 PHE 0.020 0.001 PHE A 817 TRP 0.012 0.001 TRP A 104 HIS 0.002 0.000 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00248 (27654) covalent geometry : angle 0.53049 (37613) SS BOND : bond 0.00263 ( 41) SS BOND : angle 1.08928 ( 82) hydrogen bonds : bond 0.03455 ( 989) hydrogen bonds : angle 4.80741 ( 2718) link_BETA1-4 : bond 0.00807 ( 10) link_BETA1-4 : angle 3.09752 ( 30) link_NAG-ASN : bond 0.00419 ( 28) link_NAG-ASN : angle 2.85058 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 169 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7574 (t60) REVERT: A 158 ARG cc_start: -0.1102 (OUTLIER) cc_final: -0.4987 (ttt180) REVERT: A 278 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8578 (ptmt) REVERT: A 318 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7295 (p90) REVERT: A 347 PHE cc_start: 0.4613 (OUTLIER) cc_final: 0.4357 (t80) REVERT: A 988 GLU cc_start: 0.8467 (tp30) cc_final: 0.8155 (tm-30) REVERT: A 1086 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7871 (pttm) REVERT: B 117 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 201 PHE cc_start: 0.8620 (t80) cc_final: 0.7989 (t80) REVERT: B 238 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6299 (p90) REVERT: B 303 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8894 (mt) REVERT: B 364 ASP cc_start: 0.8437 (t0) cc_final: 0.7857 (t0) REVERT: B 516 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: B 584 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8568 (tp) REVERT: B 733 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: B 988 GLU cc_start: 0.8973 (tp30) cc_final: 0.8387 (tp30) REVERT: B 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8477 (ttm) REVERT: C 113 LYS cc_start: 0.9448 (mmtm) cc_final: 0.9140 (mmmm) REVERT: C 158 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (mmm160) REVERT: C 335 LEU cc_start: 0.8490 (tt) cc_final: 0.8017 (mp) REVERT: C 555 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7263 (p) REVERT: C 590 CYS cc_start: 0.6335 (OUTLIER) cc_final: 0.6061 (m) REVERT: C 756 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8038 (t80) REVERT: D 27 ASP cc_start: 0.8348 (t0) cc_final: 0.7846 (m-30) REVERT: D 115 MET cc_start: 0.8736 (mmm) cc_final: 0.8025 (mmm) REVERT: E 56 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8036 (ttp80) REVERT: E 58 SER cc_start: 0.6444 (t) cc_final: 0.6028 (p) REVERT: E 190 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6971 (mmp80) outliers start: 144 outliers final: 94 residues processed: 294 average time/residue: 0.1693 time to fit residues: 82.0649 Evaluate side-chains 269 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 157 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 263 optimal weight: 0.2980 chunk 267 optimal weight: 0.0870 chunk 336 optimal weight: 7.9990 chunk 139 optimal weight: 0.2980 chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.117170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070414 restraints weight = 67075.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072978 restraints weight = 29140.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074705 restraints weight = 17869.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.075840 restraints weight = 13431.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076352 restraints weight = 11337.528| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27733 Z= 0.130 Angle : 0.560 11.293 37809 Z= 0.275 Chirality : 0.045 0.416 4400 Planarity : 0.003 0.050 4801 Dihedral : 6.036 58.841 4443 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 5.22 % Allowed : 24.50 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3328 helix: 2.17 (0.21), residues: 657 sheet: -0.09 (0.19), residues: 781 loop : -1.44 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.016 0.001 TYR B 365 PHE 0.025 0.001 PHE B 855 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.000 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00301 (27654) covalent geometry : angle 0.53558 (37613) SS BOND : bond 0.00204 ( 41) SS BOND : angle 1.06277 ( 82) hydrogen bonds : bond 0.03539 ( 989) hydrogen bonds : angle 4.73860 ( 2718) link_BETA1-4 : bond 0.00772 ( 10) link_BETA1-4 : angle 3.06425 ( 30) link_NAG-ASN : bond 0.00394 ( 28) link_NAG-ASN : angle 2.85224 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 165 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7954 (OUTLIER) cc_final: 0.7644 (t60) REVERT: A 158 ARG cc_start: -0.1220 (OUTLIER) cc_final: -0.5176 (ttt180) REVERT: A 278 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8572 (ptmt) REVERT: A 318 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7317 (p90) REVERT: A 347 PHE cc_start: 0.4669 (OUTLIER) cc_final: 0.4425 (t80) REVERT: A 988 GLU cc_start: 0.8489 (tp30) cc_final: 0.8173 (tm-30) REVERT: A 1086 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7858 (pttm) REVERT: B 117 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 201 PHE cc_start: 0.8597 (t80) cc_final: 0.7858 (t80) REVERT: B 238 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6386 (p90) REVERT: B 240 THR cc_start: 0.6711 (OUTLIER) cc_final: 0.6225 (t) REVERT: B 303 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8897 (mt) REVERT: B 364 ASP cc_start: 0.8451 (t0) cc_final: 0.7886 (t0) REVERT: B 571 ASP cc_start: 0.8219 (t0) cc_final: 0.7954 (t0) REVERT: B 584 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 733 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8095 (mtpt) REVERT: B 988 GLU cc_start: 0.8978 (tp30) cc_final: 0.8366 (tp30) REVERT: B 1029 MET cc_start: 0.9168 (tpp) cc_final: 0.8477 (ttm) REVERT: C 113 LYS cc_start: 0.9452 (mmtm) cc_final: 0.9128 (mmmm) REVERT: C 224 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 335 LEU cc_start: 0.8507 (tt) cc_final: 0.8038 (mp) REVERT: C 555 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 590 CYS cc_start: 0.6333 (OUTLIER) cc_final: 0.6055 (m) REVERT: C 756 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8117 (t80) REVERT: D 27 ASP cc_start: 0.8349 (t0) cc_final: 0.7845 (m-30) REVERT: D 115 MET cc_start: 0.8695 (mmm) cc_final: 0.8010 (mmm) REVERT: E 56 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: E 58 SER cc_start: 0.6450 (t) cc_final: 0.6037 (p) outliers start: 155 outliers final: 111 residues processed: 298 average time/residue: 0.1722 time to fit residues: 83.9049 Evaluate side-chains 278 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 150 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 48 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 316 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 247 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071776 restraints weight = 66577.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074334 restraints weight = 28964.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075888 restraints weight = 17432.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076821 restraints weight = 13000.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077297 restraints weight = 11071.637| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27733 Z= 0.106 Angle : 0.557 11.157 37809 Z= 0.272 Chirality : 0.045 0.416 4400 Planarity : 0.003 0.050 4801 Dihedral : 5.950 55.904 4443 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 4.38 % Allowed : 25.61 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 3328 helix: 2.23 (0.21), residues: 653 sheet: -0.06 (0.19), residues: 795 loop : -1.43 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.017 0.001 TYR B1067 PHE 0.027 0.001 PHE C 392 TRP 0.013 0.001 TRP C 353 HIS 0.003 0.000 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00242 (27654) covalent geometry : angle 0.53416 (37613) SS BOND : bond 0.00189 ( 41) SS BOND : angle 0.95504 ( 82) hydrogen bonds : bond 0.03374 ( 989) hydrogen bonds : angle 4.64172 ( 2718) link_BETA1-4 : bond 0.00824 ( 10) link_BETA1-4 : angle 2.99332 ( 30) link_NAG-ASN : bond 0.00421 ( 28) link_NAG-ASN : angle 2.80563 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 165 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7640 (t60) REVERT: A 158 ARG cc_start: -0.1219 (OUTLIER) cc_final: -0.5230 (ttt180) REVERT: A 278 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8601 (ptmt) REVERT: A 318 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7295 (p90) REVERT: A 347 PHE cc_start: 0.4432 (OUTLIER) cc_final: 0.4172 (t80) REVERT: A 562 PHE cc_start: 0.7792 (p90) cc_final: 0.7460 (p90) REVERT: A 988 GLU cc_start: 0.8477 (tp30) cc_final: 0.8166 (tm-30) REVERT: A 1086 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7863 (pttm) REVERT: B 117 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 201 PHE cc_start: 0.8524 (t80) cc_final: 0.7861 (t80) REVERT: B 238 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6339 (p90) REVERT: B 240 THR cc_start: 0.6684 (OUTLIER) cc_final: 0.6215 (t) REVERT: B 303 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8900 (mt) REVERT: B 364 ASP cc_start: 0.8361 (t0) cc_final: 0.7801 (t0) REVERT: B 516 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: B 584 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8572 (tp) REVERT: B 733 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8052 (mtpt) REVERT: B 988 GLU cc_start: 0.8970 (tp30) cc_final: 0.8403 (tp30) REVERT: B 1029 MET cc_start: 0.9138 (tpp) cc_final: 0.8489 (ttm) REVERT: C 113 LYS cc_start: 0.9451 (mmtm) cc_final: 0.9120 (mmmm) REVERT: C 157 PHE cc_start: 0.6489 (t80) cc_final: 0.6084 (t80) REVERT: C 224 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: C 335 LEU cc_start: 0.8499 (tt) cc_final: 0.8027 (mp) REVERT: C 555 SER cc_start: 0.8167 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 590 CYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5988 (m) REVERT: C 756 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8064 (t80) REVERT: D 27 ASP cc_start: 0.8315 (t0) cc_final: 0.7802 (m-30) REVERT: D 115 MET cc_start: 0.8674 (mmm) cc_final: 0.8008 (mmm) REVERT: E 56 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: E 58 SER cc_start: 0.6304 (t) cc_final: 0.5872 (p) REVERT: E 190 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6521 (mmp-170) outliers start: 130 outliers final: 96 residues processed: 274 average time/residue: 0.1721 time to fit residues: 76.8961 Evaluate side-chains 267 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 152 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 96 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C1101 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.116552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069859 restraints weight = 67325.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072424 restraints weight = 29512.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073926 restraints weight = 17972.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074999 restraints weight = 13609.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075487 restraints weight = 11558.986| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27733 Z= 0.151 Angle : 0.573 11.365 37809 Z= 0.282 Chirality : 0.045 0.411 4400 Planarity : 0.004 0.053 4801 Dihedral : 6.022 56.633 4443 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 4.58 % Allowed : 25.88 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3328 helix: 2.15 (0.21), residues: 658 sheet: -0.05 (0.19), residues: 783 loop : -1.44 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.027 0.001 TYR D 113 PHE 0.034 0.001 PHE B 855 TRP 0.010 0.001 TRP A 104 HIS 0.003 0.000 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00351 (27654) covalent geometry : angle 0.54817 (37613) SS BOND : bond 0.00205 ( 41) SS BOND : angle 1.15036 ( 82) hydrogen bonds : bond 0.03671 ( 989) hydrogen bonds : angle 4.67092 ( 2718) link_BETA1-4 : bond 0.00747 ( 10) link_BETA1-4 : angle 3.02920 ( 30) link_NAG-ASN : bond 0.00382 ( 28) link_NAG-ASN : angle 2.90833 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 157 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: -0.1245 (OUTLIER) cc_final: -0.5250 (ttt180) REVERT: A 278 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8561 (ptmt) REVERT: A 318 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7373 (p90) REVERT: A 347 PHE cc_start: 0.4626 (OUTLIER) cc_final: 0.4407 (t80) REVERT: A 988 GLU cc_start: 0.8493 (tp30) cc_final: 0.8173 (tm-30) REVERT: A 1086 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7863 (pttm) REVERT: B 117 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7307 (mm) REVERT: B 201 PHE cc_start: 0.8556 (t80) cc_final: 0.7901 (t80) REVERT: B 238 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6414 (p90) REVERT: B 240 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6249 (t) REVERT: B 364 ASP cc_start: 0.8392 (t0) cc_final: 0.7789 (t0) REVERT: B 516 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: B 571 ASP cc_start: 0.8341 (t0) cc_final: 0.7992 (t0) REVERT: B 584 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 733 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8101 (mtpt) REVERT: B 1002 GLN cc_start: 0.8497 (tt0) cc_final: 0.8232 (tt0) REVERT: B 1029 MET cc_start: 0.9183 (tpp) cc_final: 0.8551 (ttm) REVERT: C 113 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9109 (mmmm) REVERT: C 157 PHE cc_start: 0.6344 (t80) cc_final: 0.6109 (t80) REVERT: C 224 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: C 555 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7323 (p) REVERT: C 590 CYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5991 (m) REVERT: C 697 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7916 (mtm) REVERT: C 756 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8080 (t80) REVERT: D 27 ASP cc_start: 0.8327 (t0) cc_final: 0.7797 (m-30) REVERT: D 115 MET cc_start: 0.8668 (mmm) cc_final: 0.7929 (mmm) REVERT: E 56 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7911 (ttp80) outliers start: 136 outliers final: 106 residues processed: 276 average time/residue: 0.1630 time to fit residues: 73.5457 Evaluate side-chains 274 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 151 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 257 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 218 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070670 restraints weight = 66978.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073196 restraints weight = 28841.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074795 restraints weight = 17386.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075855 restraints weight = 13017.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076328 restraints weight = 11051.231| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27733 Z= 0.128 Angle : 0.567 11.167 37809 Z= 0.277 Chirality : 0.045 0.415 4400 Planarity : 0.004 0.050 4801 Dihedral : 5.894 56.069 4439 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 4.21 % Allowed : 26.35 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3328 helix: 2.19 (0.21), residues: 658 sheet: -0.02 (0.19), residues: 790 loop : -1.42 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.023 0.001 TYR E 62 PHE 0.028 0.001 PHE C 392 TRP 0.013 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00296 (27654) covalent geometry : angle 0.54314 (37613) SS BOND : bond 0.00201 ( 41) SS BOND : angle 1.10325 ( 82) hydrogen bonds : bond 0.03507 ( 989) hydrogen bonds : angle 4.61252 ( 2718) link_BETA1-4 : bond 0.00775 ( 10) link_BETA1-4 : angle 2.97727 ( 30) link_NAG-ASN : bond 0.00395 ( 28) link_NAG-ASN : angle 2.86795 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 159 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7848 (t60) REVERT: A 158 ARG cc_start: -0.1269 (OUTLIER) cc_final: -0.5349 (ttt180) REVERT: A 278 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8558 (ptmt) REVERT: A 318 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7348 (p90) REVERT: A 347 PHE cc_start: 0.4526 (OUTLIER) cc_final: 0.4294 (t80) REVERT: A 562 PHE cc_start: 0.7812 (p90) cc_final: 0.7176 (p90) REVERT: A 988 GLU cc_start: 0.8505 (tp30) cc_final: 0.8184 (tm-30) REVERT: A 1086 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7883 (pttm) REVERT: B 117 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7344 (mm) REVERT: B 201 PHE cc_start: 0.8501 (t80) cc_final: 0.7910 (t80) REVERT: B 238 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6393 (p90) REVERT: B 240 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.6272 (t) REVERT: B 364 ASP cc_start: 0.8413 (t0) cc_final: 0.7839 (t70) REVERT: B 516 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: B 571 ASP cc_start: 0.8282 (t0) cc_final: 0.8052 (t0) REVERT: B 584 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 733 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8075 (mtpt) REVERT: B 988 GLU cc_start: 0.9012 (tp30) cc_final: 0.8422 (tp30) REVERT: B 1002 GLN cc_start: 0.8478 (tt0) cc_final: 0.8218 (tt0) REVERT: B 1029 MET cc_start: 0.9158 (tpp) cc_final: 0.8548 (ttm) REVERT: C 113 LYS cc_start: 0.9461 (mmtm) cc_final: 0.9005 (mmtm) REVERT: C 157 PHE cc_start: 0.6530 (t80) cc_final: 0.6210 (t80) REVERT: C 170 TYR cc_start: 0.7097 (t80) cc_final: 0.6843 (t80) REVERT: C 224 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: C 555 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7304 (p) REVERT: C 590 CYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5979 (m) REVERT: C 697 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: C 756 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7954 (t80) REVERT: D 27 ASP cc_start: 0.8322 (t0) cc_final: 0.7778 (m-30) REVERT: E 56 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8140 (ttp80) REVERT: E 190 ARG cc_start: 0.7645 (mmp-170) cc_final: 0.7430 (mmp-170) outliers start: 125 outliers final: 97 residues processed: 266 average time/residue: 0.1667 time to fit residues: 73.3196 Evaluate side-chains 266 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 151 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 39 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 320 optimal weight: 10.0000 chunk 250 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN C1101 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.116476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069630 restraints weight = 67024.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072203 restraints weight = 28984.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073932 restraints weight = 17733.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075080 restraints weight = 13295.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075671 restraints weight = 11219.751| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27733 Z= 0.150 Angle : 0.582 13.635 37809 Z= 0.284 Chirality : 0.045 0.412 4400 Planarity : 0.004 0.051 4801 Dihedral : 5.943 56.581 4439 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 4.07 % Allowed : 26.52 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 3328 helix: 2.18 (0.21), residues: 658 sheet: -0.01 (0.19), residues: 776 loop : -1.42 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.023 0.001 TYR D 113 PHE 0.029 0.001 PHE A 817 TRP 0.012 0.001 TRP A 104 HIS 0.002 0.000 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00348 (27654) covalent geometry : angle 0.55809 (37613) SS BOND : bond 0.00201 ( 41) SS BOND : angle 1.11586 ( 82) hydrogen bonds : bond 0.03682 ( 989) hydrogen bonds : angle 4.64965 ( 2718) link_BETA1-4 : bond 0.00766 ( 10) link_BETA1-4 : angle 2.98142 ( 30) link_NAG-ASN : bond 0.00381 ( 28) link_NAG-ASN : angle 2.90475 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 160 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.7778 (t60) REVERT: A 158 ARG cc_start: -0.1166 (OUTLIER) cc_final: -0.5272 (ttt180) REVERT: A 278 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8548 (ptmt) REVERT: A 318 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7371 (p90) REVERT: A 347 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.4173 (t80) REVERT: A 562 PHE cc_start: 0.7808 (p90) cc_final: 0.7086 (p90) REVERT: A 869 MET cc_start: 0.8531 (mtm) cc_final: 0.8272 (ptp) REVERT: A 988 GLU cc_start: 0.8502 (tp30) cc_final: 0.8199 (tm-30) REVERT: A 1086 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7845 (pttm) REVERT: B 117 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7467 (mm) REVERT: B 201 PHE cc_start: 0.8537 (t80) cc_final: 0.7887 (t80) REVERT: B 238 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6407 (p90) REVERT: B 240 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6324 (t) REVERT: B 364 ASP cc_start: 0.8409 (t0) cc_final: 0.7808 (t0) REVERT: B 516 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: B 571 ASP cc_start: 0.8294 (t0) cc_final: 0.7988 (t0) REVERT: B 584 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8595 (tp) REVERT: B 733 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: B 988 GLU cc_start: 0.9004 (tp30) cc_final: 0.8409 (tp30) REVERT: B 1002 GLN cc_start: 0.8493 (tt0) cc_final: 0.8225 (tt0) REVERT: B 1029 MET cc_start: 0.9172 (tpp) cc_final: 0.8557 (ttm) REVERT: C 113 LYS cc_start: 0.9475 (mmtm) cc_final: 0.9144 (mmmm) REVERT: C 157 PHE cc_start: 0.6544 (t80) cc_final: 0.6209 (t80) REVERT: C 170 TYR cc_start: 0.7101 (t80) cc_final: 0.6822 (t80) REVERT: C 224 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: C 555 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7306 (p) REVERT: C 590 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5992 (m) REVERT: C 697 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7953 (mtm) REVERT: C 756 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8018 (t80) REVERT: C 947 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8872 (mtpp) REVERT: D 27 ASP cc_start: 0.8332 (t0) cc_final: 0.7786 (m-30) REVERT: E 56 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7671 (ttp80) outliers start: 121 outliers final: 99 residues processed: 264 average time/residue: 0.1694 time to fit residues: 73.7671 Evaluate side-chains 271 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 154 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 279 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070918 restraints weight = 66629.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073517 restraints weight = 28868.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075201 restraints weight = 17689.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076089 restraints weight = 13269.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077004 restraints weight = 11374.652| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27733 Z= 0.109 Angle : 0.577 14.160 37809 Z= 0.278 Chirality : 0.045 0.415 4400 Planarity : 0.004 0.050 4801 Dihedral : 5.822 55.861 4439 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 3.70 % Allowed : 27.16 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3328 helix: 2.28 (0.21), residues: 652 sheet: -0.00 (0.19), residues: 796 loop : -1.36 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.025 0.001 TYR D 113 PHE 0.027 0.001 PHE A 817 TRP 0.015 0.001 TRP A 104 HIS 0.002 0.000 HIS E 41 Details of bonding type rmsd covalent geometry : bond 0.00252 (27654) covalent geometry : angle 0.55510 (37613) SS BOND : bond 0.00198 ( 41) SS BOND : angle 0.98418 ( 82) hydrogen bonds : bond 0.03373 ( 989) hydrogen bonds : angle 4.54998 ( 2718) link_BETA1-4 : bond 0.00812 ( 10) link_BETA1-4 : angle 2.88405 ( 30) link_NAG-ASN : bond 0.00420 ( 28) link_NAG-ASN : angle 2.82580 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6232.36 seconds wall clock time: 107 minutes 58.58 seconds (6478.58 seconds total)