Starting phenix.real_space_refine on Mon Jul 6 19:05:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hfx_34727/07_2026/8hfx_34727.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9120 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 144 5.16 5 C 19655 2.51 5 N 5032 2.21 5 O 5975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30807 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 8 Chain: "B" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8306 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 59, 'TRANS': 998} Chain breaks: 7 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "E" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" 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 chiralities: 2 Chain: "F" 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 chiralities: 3 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 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 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 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 chiralities: 2 Chain: "O" 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 chiralities: 2 Chain: "P" 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 chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.86, per 1000 atoms: 0.19 Number of scatterers: 30807 At special positions: 0 Unit cell: (141.95, 147.9, 254.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 144 16.00 O 5975 8.00 N 5032 7.00 C 19655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.02 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A1071 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 340 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 120 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 160 " " NAG B1303 " - " ASN B 231 " " NAG B1304 " - " ASN B 279 " " NAG B1305 " - " ASN B 328 " " NAG B1306 " - " ASN B 340 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 613 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 120 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 120 " " NAG C1304 " - " ASN C 160 " " NAG C1305 " - " ASN C 231 " " NAG C1306 " - " ASN C 328 " " NAG C1307 " - " ASN C 340 " " NAG C1308 " - " ASN C 613 " " NAG D 1 " - " ASN E 54 " " NAG E 701 " - " ASN E 432 " " NAG E 702 " - " ASN E 299 " " NAG E 703 " - " ASN E 91 " " NAG F 1 " - " ASN E 546 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG L 1 " - " ASN B 714 " " NAG M 1 " - " ASN B 798 " " NAG N 1 " - " ASN B1095 " " NAG O 1 " - " ASN B1131 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN C 706 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1071 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 374 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 378 " 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 42 sheets defined 30.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.017A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.410A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.568A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.637A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.575A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.527A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.739A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 3.786A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.442A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.600A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.401A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.677A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.633A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.711A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.516A pdb=" N ARG B 902 " --> pdb=" O GLN B 898 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.697A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.699A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.861A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.700A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.455A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.605A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.958A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.685A pdb=" N ASP C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.586A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.505A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.547A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.795A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 removed outlier: 3.639A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.324A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.652A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.687A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.145A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 4.360A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 54 removed outlier: 3.581A pdb=" N ALA E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 82 removed outlier: 3.527A pdb=" N LYS E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 102 removed outlier: 3.529A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 4.038A pdb=" N ARG E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.947A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.594A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.826A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 4.253A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 4.258A pdb=" N LYS E 224 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 227 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.023A pdb=" N ASP E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 268 removed outlier: 3.688A pdb=" N GLY E 268 " --> pdb=" O HIS E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 268' Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.581A pdb=" N ASN E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 316 Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 365 through 386 removed outlier: 3.845A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 388 No H-bonds generated for 'chain 'E' and resid 387 through 388' Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.724A pdb=" N ARG E 393 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.659A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.742A pdb=" N ALA E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 449 removed outlier: 3.574A pdb=" N ILE E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.672A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.752A pdb=" N GLN E 472 " --> pdb=" O PRO E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 485 removed outlier: 3.611A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.677A pdb=" N GLU E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 533 removed outlier: 4.035A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS E 530 " --> pdb=" O HIS E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.553A pdb=" N GLN E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.347A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 574 " --> pdb=" O LEU E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 588 removed outlier: 4.450A pdb=" N ASN E 586 " --> pdb=" O LYS E 582 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 582 through 588' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.689A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.544A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 200 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.478A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 167 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.565A pdb=" N TYR A 310 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.500A pdb=" N VAL A 573 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 584 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.887A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.638A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.681A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.207A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.762A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.669A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.408A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 260 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.053A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.007A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 167 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 128 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.153A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.352A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.150A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.931A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 698 through 701 Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.962A pdb=" N GLN B1068 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 715 " --> pdb=" O PRO B1066 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 717 " --> pdb=" O TYR B1064 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B1064 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 719 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B1062 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 721 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B1060 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 723 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B1058 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1056 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.962A pdb=" N GLN B1068 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 715 " --> pdb=" O PRO B1066 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 717 " --> pdb=" O TYR B1064 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B1064 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 719 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B1062 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 721 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B1060 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 723 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B1058 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1056 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.599A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.652A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.749A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.186A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.201A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.532A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD9, first strand: chain 'C' and resid 536 through 540 removed outlier: 5.811A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.199A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.718A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.718A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AE5, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AE6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.290A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1164 hydrogen bonds defined for protein. 3228 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: 6.61 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7524 1.33 - 1.46: 8040 1.46 - 1.58: 15777 1.58 - 1.71: 0 1.71 - 1.83: 193 Bond restraints: 31534 Sorted by residual: bond pdb=" N HIS E 322 " pdb=" CA HIS E 322 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.21e-02 6.83e+03 1.38e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CA SER B 688 " pdb=" CB SER B 688 " ideal model delta sigma weight residual 1.534 1.476 0.058 1.76e-02 3.23e+03 1.07e+01 bond pdb=" N MET E 323 " pdb=" CA MET E 323 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 31529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 42132 2.34 - 4.67: 692 4.67 - 7.01: 50 7.01 - 9.34: 9 9.34 - 11.68: 2 Bond angle restraints: 42885 Sorted by residual: angle pdb=" N GLU A 337 " pdb=" CA GLU A 337 " pdb=" C GLU A 337 " ideal model delta sigma weight residual 112.93 101.25 11.68 1.33e+00 5.65e-01 7.71e+01 angle pdb=" C PRO A 334 " pdb=" CA PRO A 334 " pdb=" CB PRO A 334 " ideal model delta sigma weight residual 112.89 102.17 10.72 1.31e+00 5.83e-01 6.70e+01 angle pdb=" N PHE A 335 " pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 110.36 102.28 8.08 1.55e+00 4.16e-01 2.72e+01 angle pdb=" CA PHE A 335 " pdb=" C PHE A 335 " pdb=" O PHE A 335 " ideal model delta sigma weight residual 121.82 115.95 5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" CA PRO A 984 " pdb=" N PRO A 984 " pdb=" CD PRO A 984 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 ... (remaining 42880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16580 17.97 - 35.95: 1380 35.95 - 53.92: 242 53.92 - 71.90: 42 71.90 - 89.87: 20 Dihedral angle restraints: 18264 sinusoidal: 7223 harmonic: 11041 Sorted by residual: dihedral pdb=" CB CYS C 735 " pdb=" SG CYS C 735 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual 93.00 171.13 -78.13 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS E 530 " pdb=" SG CYS E 530 " pdb=" SG CYS E 542 " pdb=" CB CYS E 542 " ideal model delta sinusoidal sigma weight residual -86.00 -142.76 56.76 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 134 " pdb=" CB CYS C 134 " ideal model delta sinusoidal sigma weight residual -86.00 -134.55 48.55 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 18261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4655 0.097 - 0.195: 318 0.195 - 0.292: 13 0.292 - 0.390: 2 0.390 - 0.487: 3 Chirality restraints: 4991 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.67e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.56e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 ... (remaining 4988 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " -0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 984 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 541 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASN B 541 " 0.069 2.00e-02 2.50e+03 pdb=" O ASN B 541 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 542 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 503 " -0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO A 504 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " -0.045 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 745 2.69 - 3.25: 28918 3.25 - 3.80: 44512 3.80 - 4.35: 59226 4.35 - 4.90: 100415 Nonbonded interactions: 233816 Sorted by model distance: nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 2.143 3.120 nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASN B 123 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR C 89 " pdb=" OE1 GLU C 186 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN E 91 " pdb=" OG1 THR E 93 " model vdw 2.204 3.040 ... (remaining 233811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 254 or resid 259 through 1308)) selection = (chain 'B' and (resid 14 through 523 or resid 525 through 1308)) selection = (chain 'C' and (resid 14 through 254 or resid 259 through 523 or resid 525 throu \ gh 1308)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.880 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31645 Z= 0.233 Angle : 0.777 11.698 43171 Z= 0.397 Chirality : 0.052 0.487 4991 Planarity : 0.006 0.114 5441 Dihedral : 13.601 89.871 11023 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.78 % Allowed : 7.97 % Favored : 91.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3724 helix: 0.31 (0.16), residues: 977 sheet: 0.70 (0.20), residues: 657 loop : -1.14 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 67 TYR 0.025 0.002 TYR E 385 PHE 0.025 0.003 PHE C 903 TRP 0.029 0.003 TRP C 630 HIS 0.012 0.002 HIS E 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (31534) covalent geometry : angle 0.74043 / 0.39 (42885) SS BOND : bond 0.00362 / 0.23 ( 41) SS BOND : angle 1.25537 / 0.80 ( 82) hydrogen bonds : bond 0.26135 / 17.20 ( 1147) hydrogen bonds : angle 7.82842 / 5.43 ( 3228) metal coordination : bond 0.00262 / 0.14 ( 2) link_BETA1-4 : bond 0.00970 / 0.51 ( 19) link_BETA1-4 : angle 2.09161 / 1.57 ( 57) link_NAG-ASN : bond 0.00838 / 0.58 ( 49) link_NAG-ASN : angle 3.82002 / 2.54 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8120 (t0) cc_final: 0.7754 (t0) REVERT: A 342 THR cc_start: 0.4377 (OUTLIER) cc_final: 0.4030 (p) REVERT: A 406 GLN cc_start: 0.5982 (mt0) cc_final: 0.5740 (mt0) REVERT: A 495 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6279 (mpp80) REVERT: A 737 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7944 (ttp) REVERT: B 148 MET cc_start: 0.2020 (tpt) cc_final: 0.1515 (ptm) REVERT: B 344 PHE cc_start: 0.6118 (m-80) cc_final: 0.5396 (m-80) REVERT: B 357 ASN cc_start: 0.6482 (t0) cc_final: 0.6173 (t0) REVERT: C 66 HIS cc_start: 0.6805 (t70) cc_final: 0.6579 (t-170) REVERT: C 486 TYR cc_start: 0.6551 (m-80) cc_final: 0.5524 (m-80) REVERT: E 24 GLU cc_start: 0.4186 (pt0) cc_final: 0.3724 (mt-10) REVERT: E 128 TYR cc_start: 0.1588 (t80) cc_final: 0.1318 (t80) REVERT: E 225 ASP cc_start: 0.1948 (m-30) cc_final: 0.1650 (t70) REVERT: E 228 ASN cc_start: 0.6617 (p0) cc_final: 0.5648 (m-40) REVERT: E 320 LEU cc_start: 0.0325 (mm) cc_final: -0.0154 (tp) REVERT: E 351 LEU cc_start: 0.3659 (OUTLIER) cc_final: 0.3099 (tp) REVERT: E 408 MET cc_start: 0.2863 (pp-130) cc_final: 0.2314 (pmm) REVERT: E 417 TYR cc_start: 0.6136 (t80) cc_final: 0.5893 (t80) REVERT: E 508 GLU cc_start: 0.3697 (tt0) cc_final: 0.3081 (mt-10) outliers start: 26 outliers final: 9 residues processed: 266 average time/residue: 0.5135 time to fit residues: 168.4820 Evaluate side-chains 194 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 123 ASN A 191 ASN A 406 GLN A 445 ASN A 502 HIS A 577 GLN A 610 GLN A1132 ASN B 159 ASN B 357 ASN B 445 ASN B 561 GLN B 610 GLN B 759 GLN B 999 GLN C 318 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 516 HIS C 898 GLN E 50 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.168589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108653 restraints weight = 51363.963| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.21 r_work: 0.3125 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31645 Z= 0.138 Angle : 0.605 11.175 43171 Z= 0.302 Chirality : 0.046 0.437 4991 Planarity : 0.004 0.051 5441 Dihedral : 4.469 49.118 4078 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.66 % Allowed : 9.39 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.07 (0.14), residues: 3724 helix: 1.08 (0.16), residues: 1025 sheet: 0.81 (0.19), residues: 714 loop : -1.00 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.023 0.001 TYR E 510 PHE 0.030 0.001 PHE B 163 TRP 0.023 0.001 TRP B 630 HIS 0.010 0.001 HIS E 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31534) covalent geometry : angle 0.56972 / 0.29 (42885) SS BOND : bond 0.00196 / 0.13 ( 41) SS BOND : angle 0.99680 / 0.66 ( 82) hydrogen bonds : bond 0.05836 / 3.89 ( 1147) hydrogen bonds : angle 5.44069 / 3.77 ( 3228) metal coordination : bond 0.00210 / 0.10 ( 2) link_BETA1-4 : bond 0.00443 / 0.29 ( 19) link_BETA1-4 : angle 1.52864 / 1.09 ( 57) link_NAG-ASN : bond 0.00595 / 0.42 ( 49) link_NAG-ASN : angle 3.37359 / 2.40 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.5895 (OUTLIER) cc_final: 0.5523 (tp40) REVERT: A 148 MET cc_start: 0.1696 (OUTLIER) cc_final: 0.1141 (pp-130) REVERT: A 331 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7743 (t0) REVERT: A 643 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8245 (ttm170) REVERT: A 1139 GLN cc_start: 0.8400 (tp40) cc_final: 0.8098 (tm-30) REVERT: B 148 MET cc_start: 0.1917 (tpt) cc_final: 0.1203 (ptm) REVERT: B 344 PHE cc_start: 0.5893 (m-80) cc_final: 0.4895 (m-80) REVERT: B 357 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6366 (t0) REVERT: C 41 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7327 (mmtm) REVERT: C 66 HIS cc_start: 0.6744 (t70) cc_final: 0.6482 (t-170) REVERT: C 185 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6995 (mmt-90) REVERT: C 486 TYR cc_start: 0.6148 (m-80) cc_final: 0.5167 (m-80) REVERT: C 596 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8756 (p) REVERT: C 748 ASN cc_start: 0.8085 (m-40) cc_final: 0.7535 (m110) REVERT: E 196 TYR cc_start: 0.2269 (p90) cc_final: 0.1322 (m-10) REVERT: E 228 ASN cc_start: 0.6183 (p0) cc_final: 0.5750 (m-40) REVERT: E 249 MET cc_start: 0.3038 (OUTLIER) cc_final: 0.2639 (tmm) REVERT: E 320 LEU cc_start: 0.0232 (mm) cc_final: -0.0188 (tp) REVERT: E 408 MET cc_start: 0.2365 (pp-130) cc_final: 0.2052 (pmm) REVERT: E 557 MET cc_start: 0.5922 (tmm) cc_final: 0.4536 (pmm) outliers start: 55 outliers final: 22 residues processed: 219 average time/residue: 0.4830 time to fit residues: 132.0687 Evaluate side-chains 192 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1139 GLN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 321 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 314 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 445 ASN A 502 HIS A1132 ASN B 759 GLN C 311 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104898 restraints weight = 51433.415| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.65 r_work: 0.3139 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31645 Z= 0.107 Angle : 0.551 11.540 43171 Z= 0.271 Chirality : 0.045 0.448 4991 Planarity : 0.004 0.048 5441 Dihedral : 4.050 40.883 4068 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 10.89 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3724 helix: 1.42 (0.17), residues: 1021 sheet: 0.83 (0.19), residues: 724 loop : -0.93 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 405 TYR 0.016 0.001 TYR A1064 PHE 0.019 0.001 PHE B 163 TRP 0.018 0.001 TRP B 630 HIS 0.006 0.001 HIS E 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (31534) covalent geometry : angle 0.51570 / 0.26 (42885) SS BOND : bond 0.00165 / 0.11 ( 41) SS BOND : angle 1.16057 / 0.82 ( 82) hydrogen bonds : bond 0.04718 / 3.15 ( 1147) hydrogen bonds : angle 4.99337 / 3.45 ( 3228) metal coordination : bond 0.00678 / 0.35 ( 2) link_BETA1-4 : bond 0.00323 / 0.21 ( 19) link_BETA1-4 : angle 1.49304 / 1.06 ( 57) link_NAG-ASN : bond 0.00547 / 0.40 ( 49) link_NAG-ASN : angle 3.13957 / 2.17 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5684 (tp40) REVERT: A 148 MET cc_start: 0.1756 (pmm) cc_final: 0.1156 (pp-130) REVERT: A 331 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 445 ASN cc_start: 0.7115 (t0) cc_final: 0.6731 (m-40) REVERT: A 495 ARG cc_start: 0.7094 (mtt90) cc_final: 0.6269 (mpp80) REVERT: A 1139 GLN cc_start: 0.8388 (tp40) cc_final: 0.8080 (tm-30) REVERT: B 148 MET cc_start: 0.1829 (tpt) cc_final: 0.1173 (ptm) REVERT: B 344 PHE cc_start: 0.5945 (m-80) cc_final: 0.4947 (m-80) REVERT: B 583 ASP cc_start: 0.7734 (m-30) cc_final: 0.7275 (m-30) REVERT: B 970 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7460 (pp) REVERT: C 41 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7356 (mmtm) REVERT: C 66 HIS cc_start: 0.6593 (t70) cc_final: 0.6300 (t-170) REVERT: C 185 ARG cc_start: 0.7247 (mmt180) cc_final: 0.7000 (mmt-90) REVERT: C 354 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7627 (ttm170) REVERT: C 371 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6706 (p90) REVERT: C 417 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8040 (p0) REVERT: C 486 TYR cc_start: 0.6255 (m-80) cc_final: 0.5307 (m-80) REVERT: C 748 ASN cc_start: 0.8111 (m-40) cc_final: 0.7651 (m110) REVERT: E 196 TYR cc_start: 0.2391 (p90) cc_final: 0.1368 (m-10) REVERT: E 228 ASN cc_start: 0.6085 (p0) cc_final: 0.5610 (m-40) REVERT: E 274 PHE cc_start: 0.5013 (t80) cc_final: 0.4736 (t80) REVERT: E 320 LEU cc_start: 0.0260 (mm) cc_final: -0.0194 (tp) REVERT: E 374 HIS cc_start: 0.1957 (t-170) cc_final: 0.1301 (t-170) REVERT: E 474 MET cc_start: 0.0839 (tpt) cc_final: -0.1588 (mpt) REVERT: E 557 MET cc_start: 0.6129 (tmm) cc_final: 0.4729 (pmm) REVERT: E 571 GLU cc_start: 0.2613 (mt-10) cc_final: 0.2327 (pt0) outliers start: 45 outliers final: 18 residues processed: 210 average time/residue: 0.5480 time to fit residues: 141.5198 Evaluate side-chains 189 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 217 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 502 HIS A 752 GLN A 801 GLN B 625 GLN B 748 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.164577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103966 restraints weight = 50880.269| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.10 r_work: 0.3074 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 31645 Z= 0.231 Angle : 0.643 12.359 43171 Z= 0.319 Chirality : 0.049 0.447 4991 Planarity : 0.005 0.048 5441 Dihedral : 4.415 36.677 4065 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.26 % Allowed : 11.89 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.12 (0.14), residues: 3724 helix: 1.18 (0.16), residues: 1028 sheet: 0.69 (0.19), residues: 733 loop : -1.10 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.023 0.002 TYR B1064 PHE 0.033 0.002 PHE B 903 TRP 0.025 0.002 TRP B 883 HIS 0.006 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (31534) covalent geometry : angle 0.61354 / 0.31 (42885) SS BOND : bond 0.00283 / 0.17 ( 41) SS BOND : angle 1.45156 / 0.98 ( 82) hydrogen bonds : bond 0.05784 / 3.89 ( 1147) hydrogen bonds : angle 5.05449 / 3.50 ( 3228) metal coordination : bond 0.00283 / 0.14 ( 2) link_BETA1-4 : bond 0.00334 / 0.22 ( 19) link_BETA1-4 : angle 1.63646 / 1.18 ( 57) link_NAG-ASN : bond 0.00497 / 0.34 ( 49) link_NAG-ASN : angle 3.08670 / 2.17 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 126 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 148 MET cc_start: 0.1722 (OUTLIER) cc_final: 0.0279 (pmm) REVERT: A 331 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7897 (t0) REVERT: A 445 ASN cc_start: 0.7134 (t0) cc_final: 0.6690 (m-40) REVERT: A 495 ARG cc_start: 0.7125 (mtt90) cc_final: 0.6303 (mpp80) REVERT: A 1139 GLN cc_start: 0.8343 (tp40) cc_final: 0.7994 (tm-30) REVERT: B 148 MET cc_start: 0.1625 (tpt) cc_final: 0.1103 (ptm) REVERT: B 970 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7751 (pp) REVERT: C 41 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7655 (mmtm) REVERT: C 66 HIS cc_start: 0.6684 (t70) cc_final: 0.6471 (t-170) REVERT: C 185 ARG cc_start: 0.7318 (mmt180) cc_final: 0.7065 (mmt-90) REVERT: C 371 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 405 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7461 (ptm160) REVERT: C 737 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (ttp) REVERT: E 196 TYR cc_start: 0.2338 (p90) cc_final: 0.1348 (m-10) REVERT: E 228 ASN cc_start: 0.6034 (p0) cc_final: 0.5571 (m-40) REVERT: E 274 PHE cc_start: 0.5072 (t80) cc_final: 0.4778 (t80) REVERT: E 291 ILE cc_start: 0.3400 (OUTLIER) cc_final: 0.3021 (tp) REVERT: E 320 LEU cc_start: 0.0239 (mm) cc_final: -0.0202 (tp) REVERT: E 323 MET cc_start: -0.1089 (ppp) cc_final: -0.1416 (ppp) REVERT: E 324 THR cc_start: 0.5101 (t) cc_final: 0.4261 (p) REVERT: E 325 GLN cc_start: 0.6571 (mt0) cc_final: 0.5912 (mp10) REVERT: E 557 MET cc_start: 0.6252 (tmm) cc_final: 0.4822 (pmm) REVERT: E 571 GLU cc_start: 0.2834 (mt-10) cc_final: 0.2615 (pt0) outliers start: 75 outliers final: 29 residues processed: 210 average time/residue: 0.5583 time to fit residues: 144.1182 Evaluate side-chains 197 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 HIS B 625 GLN B 759 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN E 35 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.166161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106633 restraints weight = 51224.933| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.15 r_work: 0.3105 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31645 Z= 0.127 Angle : 0.554 11.221 43171 Z= 0.273 Chirality : 0.045 0.475 4991 Planarity : 0.004 0.048 5441 Dihedral : 4.138 26.151 4065 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.69 % Allowed : 13.03 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.04 (0.14), residues: 3724 helix: 1.43 (0.17), residues: 1021 sheet: 0.77 (0.19), residues: 725 loop : -1.04 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 405 TYR 0.017 0.001 TYR C1064 PHE 0.015 0.001 PHE A1118 TRP 0.017 0.001 TRP B 630 HIS 0.006 0.001 HIS E 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (31534) covalent geometry : angle 0.52442 / 0.27 (42885) SS BOND : bond 0.00207 / 0.14 ( 41) SS BOND : angle 1.13741 / 0.74 ( 82) hydrogen bonds : bond 0.04582 / 3.08 ( 1147) hydrogen bonds : angle 4.81596 / 3.34 ( 3228) metal coordination : bond 0.00140 / 0.07 ( 2) link_BETA1-4 : bond 0.00370 / 0.24 ( 19) link_BETA1-4 : angle 1.48687 / 1.07 ( 57) link_NAG-ASN : bond 0.00477 / 0.32 ( 49) link_NAG-ASN : angle 2.88083 / 2.00 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 445 ASN cc_start: 0.7108 (t0) cc_final: 0.6716 (m-40) REVERT: A 495 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6258 (mpp80) REVERT: A 1139 GLN cc_start: 0.8322 (tp40) cc_final: 0.8070 (tm-30) REVERT: B 148 MET cc_start: 0.1624 (tpt) cc_final: 0.1037 (ptm) REVERT: B 583 ASP cc_start: 0.7715 (m-30) cc_final: 0.7283 (m-30) REVERT: C 41 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7341 (mmtm) REVERT: C 66 HIS cc_start: 0.6747 (t70) cc_final: 0.6306 (t-170) REVERT: C 185 ARG cc_start: 0.7296 (mmt180) cc_final: 0.7050 (mmt-90) REVERT: C 371 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6739 (p90) REVERT: C 405 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7525 (ptm160) REVERT: E 196 TYR cc_start: 0.2295 (p90) cc_final: 0.1480 (m-10) REVERT: E 228 ASN cc_start: 0.5983 (p0) cc_final: 0.5516 (m-40) REVERT: E 249 MET cc_start: 0.2851 (OUTLIER) cc_final: 0.2472 (tmm) REVERT: E 274 PHE cc_start: 0.5082 (t80) cc_final: 0.4792 (t80) REVERT: E 291 ILE cc_start: 0.3452 (OUTLIER) cc_final: 0.3040 (tp) REVERT: E 320 LEU cc_start: 0.0271 (mm) cc_final: -0.0159 (tp) REVERT: E 323 MET cc_start: -0.0960 (ppp) cc_final: -0.1354 (ppp) REVERT: E 324 THR cc_start: 0.4938 (t) cc_final: 0.4142 (p) REVERT: E 325 GLN cc_start: 0.6517 (mt0) cc_final: 0.5825 (mp10) REVERT: E 474 MET cc_start: 0.0515 (tpt) cc_final: -0.1772 (mpt) REVERT: E 557 MET cc_start: 0.6149 (tmm) cc_final: 0.4714 (pmm) REVERT: E 571 GLU cc_start: 0.2973 (mt-10) cc_final: 0.2673 (pt0) outliers start: 56 outliers final: 28 residues processed: 206 average time/residue: 0.5574 time to fit residues: 141.3877 Evaluate side-chains 191 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 296 optimal weight: 7.9990 chunk 327 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 HIS C 445 ASN C 898 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.164813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104755 restraints weight = 51008.330| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.08 r_work: 0.3088 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31645 Z= 0.176 Angle : 0.590 12.008 43171 Z= 0.292 Chirality : 0.047 0.484 4991 Planarity : 0.004 0.049 5441 Dihedral : 4.210 19.992 4065 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.99 % Allowed : 13.36 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.05 (0.14), residues: 3724 helix: 1.37 (0.17), residues: 1022 sheet: 0.70 (0.19), residues: 731 loop : -1.12 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 405 TYR 0.022 0.001 TYR A 165 PHE 0.025 0.002 PHE A 163 TRP 0.024 0.001 TRP E 49 HIS 0.009 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (31534) covalent geometry : angle 0.56371 / 0.29 (42885) SS BOND : bond 0.00228 / 0.14 ( 41) SS BOND : angle 1.27601 / 0.85 ( 82) hydrogen bonds : bond 0.05031 / 3.39 ( 1147) hydrogen bonds : angle 4.83417 / 3.35 ( 3228) metal coordination : bond 0.03431 / 1.65 ( 2) link_BETA1-4 : bond 0.00360 / 0.23 ( 19) link_BETA1-4 : angle 1.51209 / 1.09 ( 57) link_NAG-ASN : bond 0.00469 / 0.31 ( 49) link_NAG-ASN : angle 2.77542 / 1.96 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 445 ASN cc_start: 0.7134 (t0) cc_final: 0.6776 (m-40) REVERT: A 1139 GLN cc_start: 0.8327 (tp40) cc_final: 0.8045 (tm-30) REVERT: B 148 MET cc_start: 0.1595 (tpt) cc_final: 0.1159 (ptm) REVERT: B 748 ASN cc_start: 0.9018 (m-40) cc_final: 0.8689 (t0) REVERT: C 41 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7524 (mmtm) REVERT: C 66 HIS cc_start: 0.6682 (t70) cc_final: 0.6224 (t-170) REVERT: C 185 ARG cc_start: 0.7305 (mmt180) cc_final: 0.7057 (mmt-90) REVERT: C 371 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6746 (p90) REVERT: C 405 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: E 196 TYR cc_start: 0.2277 (p90) cc_final: 0.1597 (m-10) REVERT: E 249 MET cc_start: 0.2889 (OUTLIER) cc_final: 0.2480 (tmm) REVERT: E 274 PHE cc_start: 0.5070 (t80) cc_final: 0.4771 (t80) REVERT: E 291 ILE cc_start: 0.3502 (OUTLIER) cc_final: 0.3131 (tp) REVERT: E 323 MET cc_start: -0.0536 (ppp) cc_final: -0.0948 (ppp) REVERT: E 324 THR cc_start: 0.4962 (t) cc_final: 0.4158 (p) REVERT: E 325 GLN cc_start: 0.6521 (mt0) cc_final: 0.5816 (mp10) REVERT: E 557 MET cc_start: 0.6084 (tmm) cc_final: 0.4657 (pmm) REVERT: E 571 GLU cc_start: 0.2989 (mt-10) cc_final: 0.2716 (pt0) outliers start: 66 outliers final: 41 residues processed: 211 average time/residue: 0.5528 time to fit residues: 144.2741 Evaluate side-chains 199 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 161 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 329 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 391 ASN A 502 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.165854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105887 restraints weight = 51202.314| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.06 r_work: 0.3110 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31645 Z= 0.126 Angle : 0.546 10.936 43171 Z= 0.269 Chirality : 0.045 0.490 4991 Planarity : 0.004 0.049 5441 Dihedral : 4.031 21.998 4064 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.81 % Allowed : 14.29 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.07 (0.14), residues: 3724 helix: 1.52 (0.17), residues: 1017 sheet: 0.74 (0.19), residues: 727 loop : -1.05 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 405 TYR 0.017 0.001 TYR C1064 PHE 0.016 0.001 PHE A1118 TRP 0.023 0.001 TRP E 49 HIS 0.010 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (31534) covalent geometry : angle 0.52122 / 0.26 (42885) SS BOND : bond 0.00187 / 0.12 ( 41) SS BOND : angle 1.06780 / 0.71 ( 82) hydrogen bonds : bond 0.04317 / 2.91 ( 1147) hydrogen bonds : angle 4.69873 / 3.26 ( 3228) metal coordination : bond 0.00664 / 0.34 ( 2) link_BETA1-4 : bond 0.00369 / 0.24 ( 19) link_BETA1-4 : angle 1.41846 / 1.02 ( 57) link_NAG-ASN : bond 0.00455 / 0.30 ( 49) link_NAG-ASN : angle 2.65161 / 1.88 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7790 (t0) REVERT: A 418 TYR cc_start: 0.6703 (m-80) cc_final: 0.6375 (m-80) REVERT: A 445 ASN cc_start: 0.7112 (t0) cc_final: 0.6676 (m-40) REVERT: A 1139 GLN cc_start: 0.8315 (tp40) cc_final: 0.8045 (tm-30) REVERT: B 148 MET cc_start: 0.1274 (tpt) cc_final: 0.1010 (ptm) REVERT: B 583 ASP cc_start: 0.7700 (m-30) cc_final: 0.7298 (m-30) REVERT: B 748 ASN cc_start: 0.9028 (m-40) cc_final: 0.8711 (t0) REVERT: B 982 ASP cc_start: 0.6337 (p0) cc_final: 0.5904 (p0) REVERT: C 41 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7616 (mmtm) REVERT: C 66 HIS cc_start: 0.6526 (t70) cc_final: 0.6055 (t-170) REVERT: C 185 ARG cc_start: 0.7342 (mmt180) cc_final: 0.7101 (mmt-90) REVERT: C 371 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6679 (p90) REVERT: C 405 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: E 196 TYR cc_start: 0.2412 (p90) cc_final: 0.1778 (m-10) REVERT: E 274 PHE cc_start: 0.5111 (t80) cc_final: 0.4841 (t80) REVERT: E 291 ILE cc_start: 0.3438 (OUTLIER) cc_final: 0.3012 (tp) REVERT: E 323 MET cc_start: -0.0729 (ppp) cc_final: -0.1038 (ppp) REVERT: E 324 THR cc_start: 0.4765 (t) cc_final: 0.3999 (p) REVERT: E 325 GLN cc_start: 0.6384 (mt0) cc_final: 0.5733 (mp10) REVERT: E 474 MET cc_start: 0.0369 (tpt) cc_final: -0.1798 (mpt) REVERT: E 557 MET cc_start: 0.6162 (tmm) cc_final: 0.4779 (pmm) REVERT: E 571 GLU cc_start: 0.3042 (mt-10) cc_final: 0.2750 (pt0) outliers start: 60 outliers final: 37 residues processed: 210 average time/residue: 0.4920 time to fit residues: 128.4583 Evaluate side-chains 200 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 256 optimal weight: 3.9990 chunk 329 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN A 502 HIS C 898 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103784 restraints weight = 51211.826| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.07 r_work: 0.3071 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31645 Z= 0.213 Angle : 0.616 11.293 43171 Z= 0.304 Chirality : 0.048 0.491 4991 Planarity : 0.004 0.048 5441 Dihedral : 4.284 19.190 4063 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.96 % Allowed : 14.14 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.10 (0.14), residues: 3724 helix: 1.36 (0.17), residues: 1020 sheet: 0.64 (0.19), residues: 727 loop : -1.14 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.021 0.002 TYR C 262 PHE 0.020 0.002 PHE A1118 TRP 0.019 0.001 TRP E 49 HIS 0.009 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.21 (31534) covalent geometry : angle 0.59043 / 0.30 (42885) SS BOND : bond 0.00292 / 0.17 ( 41) SS BOND : angle 1.40568 / 0.94 ( 82) hydrogen bonds : bond 0.05304 / 3.57 ( 1147) hydrogen bonds : angle 4.86847 / 3.38 ( 3228) metal coordination : bond 0.00244 / 0.13 ( 2) link_BETA1-4 : bond 0.00393 / 0.25 ( 19) link_BETA1-4 : angle 1.51707 / 1.10 ( 57) link_NAG-ASN : bond 0.00474 / 0.31 ( 49) link_NAG-ASN : angle 2.78475 / 1.97 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7508 (t-90) REVERT: A 148 MET cc_start: 0.1860 (OUTLIER) cc_final: 0.0494 (pmm) REVERT: A 331 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7866 (t0) REVERT: A 445 ASN cc_start: 0.7099 (t0) cc_final: 0.6655 (m-40) REVERT: B 148 MET cc_start: 0.1133 (tpt) cc_final: 0.0817 (ptm) REVERT: B 748 ASN cc_start: 0.9028 (m-40) cc_final: 0.8714 (t0) REVERT: B 982 ASP cc_start: 0.6279 (p0) cc_final: 0.5873 (p0) REVERT: C 41 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7635 (mptt) REVERT: C 127 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7537 (ttpp) REVERT: C 371 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6631 (p90) REVERT: C 405 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7574 (ptm160) REVERT: E 196 TYR cc_start: 0.2373 (p90) cc_final: 0.1757 (m-10) REVERT: E 274 PHE cc_start: 0.5080 (t80) cc_final: 0.4810 (t80) REVERT: E 291 ILE cc_start: 0.3704 (OUTLIER) cc_final: 0.3288 (tp) REVERT: E 325 GLN cc_start: 0.6487 (mt0) cc_final: 0.5757 (mp10) REVERT: E 557 MET cc_start: 0.6170 (tmm) cc_final: 0.4788 (pmm) REVERT: E 571 GLU cc_start: 0.2952 (mt-10) cc_final: 0.2675 (pt0) outliers start: 65 outliers final: 41 residues processed: 206 average time/residue: 0.5403 time to fit residues: 137.7665 Evaluate side-chains 202 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 152 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 205 optimal weight: 0.0670 chunk 228 optimal weight: 0.0370 chunk 227 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS B 759 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN E 35 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097466 restraints weight = 51078.878| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.01 r_work: 0.3113 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31645 Z= 0.121 Angle : 0.559 14.332 43171 Z= 0.274 Chirality : 0.045 0.496 4991 Planarity : 0.004 0.049 5441 Dihedral : 4.066 20.858 4063 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.44 % Allowed : 14.93 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.06 (0.14), residues: 3724 helix: 1.52 (0.17), residues: 1018 sheet: 0.71 (0.19), residues: 735 loop : -1.05 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 980 TYR 0.017 0.001 TYR C1064 PHE 0.015 0.001 PHE A1118 TRP 0.016 0.001 TRP B 630 HIS 0.010 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (31534) covalent geometry : angle 0.53448 / 0.27 (42885) SS BOND : bond 0.00288 / 0.21 ( 41) SS BOND : angle 1.14325 / 0.75 ( 82) hydrogen bonds : bond 0.04282 / 2.88 ( 1147) hydrogen bonds : angle 4.69158 / 3.25 ( 3228) metal coordination : bond 0.00113 / 0.06 ( 2) link_BETA1-4 : bond 0.00373 / 0.24 ( 19) link_BETA1-4 : angle 1.41256 / 1.02 ( 57) link_NAG-ASN : bond 0.00462 / 0.31 ( 49) link_NAG-ASN : angle 2.65320 / 1.89 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7692 (t-90) cc_final: 0.7348 (t-90) REVERT: A 148 MET cc_start: 0.1829 (OUTLIER) cc_final: 0.0564 (pmm) REVERT: A 331 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7888 (t0) REVERT: A 445 ASN cc_start: 0.7094 (t0) cc_final: 0.6655 (m-40) REVERT: A 580 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: A 631 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.5068 (tmt-80) REVERT: A 1139 GLN cc_start: 0.8449 (tp40) cc_final: 0.8103 (tm-30) REVERT: B 148 MET cc_start: 0.1098 (tpt) cc_final: 0.0822 (ptm) REVERT: B 748 ASN cc_start: 0.9081 (m-40) cc_final: 0.8734 (t0) REVERT: B 982 ASP cc_start: 0.6148 (p0) cc_final: 0.5710 (p0) REVERT: C 41 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7704 (mptt) REVERT: C 127 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7441 (ttpp) REVERT: C 185 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7272 (mmt-90) REVERT: C 405 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7583 (ptm160) REVERT: E 196 TYR cc_start: 0.2353 (p90) cc_final: 0.1758 (m-10) REVERT: E 274 PHE cc_start: 0.5070 (t80) cc_final: 0.4780 (t80) REVERT: E 291 ILE cc_start: 0.3663 (OUTLIER) cc_final: 0.3216 (tp) REVERT: E 324 THR cc_start: 0.4885 (t) cc_final: 0.4081 (p) REVERT: E 325 GLN cc_start: 0.6457 (mt0) cc_final: 0.5728 (mp10) REVERT: E 474 MET cc_start: 0.0487 (tpt) cc_final: -0.1721 (mpt) REVERT: E 557 MET cc_start: 0.6117 (tmm) cc_final: 0.4778 (pmm) REVERT: E 571 GLU cc_start: 0.3054 (mt-10) cc_final: 0.2794 (pt0) outliers start: 48 outliers final: 35 residues processed: 197 average time/residue: 0.5666 time to fit residues: 137.1741 Evaluate side-chains 194 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 304 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 242 optimal weight: 0.0970 chunk 352 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 chunk 180 optimal weight: 0.0040 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN A 502 HIS B1139 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.165401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105320 restraints weight = 50722.247| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.08 r_work: 0.3115 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31645 Z= 0.130 Angle : 0.564 15.587 43171 Z= 0.276 Chirality : 0.045 0.493 4991 Planarity : 0.004 0.048 5441 Dihedral : 4.018 21.559 4063 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.44 % Allowed : 14.87 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.10 (0.14), residues: 3724 helix: 1.56 (0.17), residues: 1018 sheet: 0.70 (0.19), residues: 742 loop : -1.02 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 405 TYR 0.021 0.001 TYR A 165 PHE 0.028 0.001 PHE A 163 TRP 0.015 0.001 TRP E 49 HIS 0.009 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (31534) covalent geometry : angle 0.53979 / 0.27 (42885) SS BOND : bond 0.00302 / 0.17 ( 41) SS BOND : angle 1.05741 / 0.67 ( 82) hydrogen bonds : bond 0.04292 / 2.89 ( 1147) hydrogen bonds : angle 4.67189 / 3.24 ( 3228) metal coordination : bond 0.00106 / 0.06 ( 2) link_BETA1-4 : bond 0.00389 / 0.24 ( 19) link_BETA1-4 : angle 1.38740 / 1.00 ( 57) link_NAG-ASN : bond 0.00457 / 0.30 ( 49) link_NAG-ASN : angle 2.62351 / 1.87 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7264 (t-90) REVERT: A 331 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 445 ASN cc_start: 0.7090 (t0) cc_final: 0.6628 (m-40) REVERT: A 580 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: A 631 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.5086 (tmt-80) REVERT: A 1139 GLN cc_start: 0.8463 (tp40) cc_final: 0.8101 (tm-30) REVERT: B 148 MET cc_start: 0.1189 (tpt) cc_final: 0.0895 (ptm) REVERT: B 748 ASN cc_start: 0.9084 (m-40) cc_final: 0.8740 (t0) REVERT: B 982 ASP cc_start: 0.6056 (p0) cc_final: 0.5608 (p0) REVERT: C 41 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7706 (mptt) REVERT: C 127 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7520 (ttpp) REVERT: C 185 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7318 (mmt-90) REVERT: C 405 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: E 196 TYR cc_start: 0.2382 (p90) cc_final: 0.1802 (m-10) REVERT: E 289 PRO cc_start: 0.5952 (Cg_exo) cc_final: 0.5710 (Cg_endo) REVERT: E 291 ILE cc_start: 0.3654 (OUTLIER) cc_final: 0.3210 (tp) REVERT: E 324 THR cc_start: 0.4961 (t) cc_final: 0.4117 (p) REVERT: E 325 GLN cc_start: 0.6472 (mt0) cc_final: 0.5751 (mp10) REVERT: E 474 MET cc_start: 0.0405 (tpt) cc_final: -0.1748 (mpt) REVERT: E 557 MET cc_start: 0.6168 (tmm) cc_final: 0.4889 (pmm) REVERT: E 571 GLU cc_start: 0.3015 (mt-10) cc_final: 0.2759 (pt0) outliers start: 48 outliers final: 38 residues processed: 191 average time/residue: 0.5145 time to fit residues: 120.0969 Evaluate side-chains 194 residues out of total 3323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 6 optimal weight: 0.9980 chunk 291 optimal weight: 0.0270 chunk 245 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN A 502 HIS B1139 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.166323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107504 restraints weight = 51053.166| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.09 r_work: 0.3125 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 31645 Z= 0.104 Angle : 0.544 15.604 43171 Z= 0.266 Chirality : 0.045 0.490 4991 Planarity : 0.004 0.049 5441 Dihedral : 3.915 23.499 4063 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 14.87 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.19 (0.14), residues: 3724 helix: 1.65 (0.17), residues: 1015 sheet: 0.74 (0.19), residues: 732 loop : -0.97 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 405 TYR 0.017 0.001 TYR C1064 PHE 0.013 0.001 PHE A 339 TRP 0.015 0.001 TRP B 630 HIS 0.010 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (31534) covalent geometry : angle 0.52029 / 0.26 (42885) SS BOND : bond 0.00194 / 0.13 ( 41) SS BOND : angle 0.94933 / 0.60 ( 82) hydrogen bonds : bond 0.03890 / 2.61 ( 1147) hydrogen bonds : angle 4.59210 / 3.18 ( 3228) metal coordination : bond 0.00070 / 0.04 ( 2) link_BETA1-4 : bond 0.00399 / 0.25 ( 19) link_BETA1-4 : angle 1.35833 / 0.97 ( 57) link_NAG-ASN : bond 0.00470 / 0.31 ( 49) link_NAG-ASN : angle 2.56944 / 1.83 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10065.53 seconds wall clock time: 172 minutes 11.64 seconds (10331.64 seconds total)