Starting phenix.real_space_refine on Mon Aug 25 09:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmn_61607/08_2025/9jmn_61607.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 16978 2.51 5 N 4394 2.21 5 O 5290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26833 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8679 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 46, 'TRANS': 1063} Chain breaks: 10 Chain: "B" Number of atoms: 8679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8679 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 46, 'TRANS': 1063} Chain breaks: 10 Chain: "C" Number of atoms: 8679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8679 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 46, 'TRANS': 1063} Chain breaks: 10 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 198 Unusual residues: {'EIC': 2, 'FOL': 1, 'NAG': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 164 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'FOL': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.17, per 1000 atoms: 0.19 Number of scatterers: 26833 At special positions: 0 Unit cell: (142.56, 151.8, 157.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5290 8.00 N 4394 7.00 C 16978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 338 " distance=2.02 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 396 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS A 467 " distance=2.05 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 572 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 642 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 638 " distance=2.03 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 699 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 722 " distance=2.03 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 796 " distance=2.03 Simple disulfide: pdb=" SG CYS A 892 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1097 " distance=2.03 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 225 " distance=2.05 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 396 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 572 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 638 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS B 785 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 790 " - pdb=" SG CYS B 796 " distance=2.03 Simple disulfide: pdb=" SG CYS B 892 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1097 " distance=2.03 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 338 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 467 " distance=2.05 Simple disulfide: pdb=" SG CYS C 426 " - pdb=" SG CYS C 572 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 638 " distance=2.03 Simple disulfide: pdb=" SG CYS C 667 " - pdb=" SG CYS C 699 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 722 " distance=2.03 Simple disulfide: pdb=" SG CYS C 785 " - pdb=" SG CYS C 807 " distance=2.03 Simple disulfide: pdb=" SG CYS C 790 " - pdb=" SG CYS C 796 " distance=2.03 Simple disulfide: pdb=" SG CYS C 892 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C1086 " - pdb=" SG CYS C1097 " distance=2.03 Simple disulfide: pdb=" SG CYS C1136 " - pdb=" SG CYS C1143 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A1401 " - " ASN A 41 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 97 " " NAG A1404 " - " ASN A 158 " " NAG A1405 " - " ASN A 232 " " NAG A1406 " - " ASN A 387 " " NAG A1408 " - " ASN A 849 " " NAG A1409 " - " ASN A1188 " " NAG B1401 " - " ASN B 41 " " NAG B1402 " - " ASN B 58 " " NAG B1403 " - " ASN B 97 " " NAG B1404 " - " ASN B 158 " " NAG B1405 " - " ASN B 232 " " NAG B1406 " - " ASN B 849 " " NAG B1408 " - " ASN B 705 " " NAG B1409 " - " ASN B1188 " " NAG C1401 " - " ASN C 41 " " NAG C1402 " - " ASN C 58 " " NAG C1403 " - " ASN C 97 " " NAG C1404 " - " ASN C 158 " " NAG C1405 " - " ASN C 232 " " NAG C1406 " - " ASN C 849 " " NAG C1407 " - " ASN C1188 " " NAG C1409 " - " ASN C 705 " " NAG D 1 " - " ASN A 399 " " NAG E 1 " - " ASN A 118 " " NAG F 1 " - " ASN B 118 " " NAG G 1 " - " ASN B 387 " " NAG H 1 " - " ASN B 399 " " NAG I 1 " - " ASN C 118 " " NAG J 1 " - " ASN C 387 " " NAG K 1 " - " ASN C 399 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 706.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1410 " pdb=" CB FOL B1407 " pdb=" CB FOL C1408 " Number of C-beta restraints generated: 6228 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 65 sheets defined 26.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 331 through 341 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.709A pdb=" N VAL A 376 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 438 through 446 removed outlier: 5.204A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.531A pdb=" N LEU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.773A pdb=" N LEU A 588 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 673 removed outlier: 4.142A pdb=" N ILE A 673 " --> pdb=" O HIS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 790 Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 806 through 833 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 920 through 933 Processing helix chain 'A' and resid 951 through 964 removed outlier: 3.737A pdb=" N GLY A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 964 " --> pdb=" O MET A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 removed outlier: 3.840A pdb=" N LEU A 970 " --> pdb=" O THR A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 990 Processing helix chain 'A' and resid 996 through 1018 removed outlier: 3.838A pdb=" N LYS A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A1003 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1038 removed outlier: 3.601A pdb=" N ARG A1037 " --> pdb=" O ASP A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1087 removed outlier: 3.662A pdb=" N GLU A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 331 through 341 Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.514A pdb=" N LYS B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.656A pdb=" N LEU B 403 " --> pdb=" O ASN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 474 through 481 Processing helix chain 'B' and resid 512 through 522 removed outlier: 3.557A pdb=" N LEU B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 673 removed outlier: 3.554A pdb=" N ILE B 673 " --> pdb=" O HIS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 790 Processing helix chain 'B' and resid 793 through 803 Processing helix chain 'B' and resid 806 through 833 Processing helix chain 'B' and resid 838 through 842 removed outlier: 3.599A pdb=" N ALA B 842 " --> pdb=" O PRO B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.532A pdb=" N VAL B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 910 removed outlier: 3.596A pdb=" N TYR B 908 " --> pdb=" O CYS B 905 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 909 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 910 " --> pdb=" O GLN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 905 through 910' Processing helix chain 'B' and resid 920 through 932 Processing helix chain 'B' and resid 951 through 962 removed outlier: 3.831A pdb=" N GLY B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 973 removed outlier: 3.581A pdb=" N LEU B 970 " --> pdb=" O THR B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 992 removed outlier: 3.850A pdb=" N PHE B 992 " --> pdb=" O MET B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1018 removed outlier: 3.881A pdb=" N VAL B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B1013 " --> pdb=" O ASN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1022 removed outlier: 3.772A pdb=" N ASN B1022 " --> pdb=" O GLU B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1019 through 1022' Processing helix chain 'B' and resid 1030 through 1038 Processing helix chain 'B' and resid 1039 through 1087 removed outlier: 4.259A pdb=" N VAL B1045 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B1070 " --> pdb=" O LEU B1066 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B1071 " --> pdb=" O VAL B1067 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1087 " --> pdb=" O VAL B1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.935A pdb=" N GLN C 33 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 331 through 340 Processing helix chain 'C' and resid 373 through 378 removed outlier: 3.951A pdb=" N VAL C 376 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 418 through 425 Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.614A pdb=" N MET C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 481 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.844A pdb=" N LEU C 588 " --> pdb=" O ASP C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 673 removed outlier: 3.695A pdb=" N ILE C 673 " --> pdb=" O HIS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 790 removed outlier: 3.553A pdb=" N VAL C 789 " --> pdb=" O CYS C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 803 Processing helix chain 'C' and resid 806 through 833 Processing helix chain 'C' and resid 838 through 844 removed outlier: 4.389A pdb=" N ALA C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 843 " --> pdb=" O PRO C 839 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 844 " --> pdb=" O LEU C 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 838 through 844' Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 868 through 877 Processing helix chain 'C' and resid 904 through 911 Processing helix chain 'C' and resid 920 through 932 removed outlier: 3.519A pdb=" N LEU C 931 " --> pdb=" O TYR C 927 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 932 " --> pdb=" O THR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 964 removed outlier: 3.752A pdb=" N GLY C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 963 " --> pdb=" O ARG C 959 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY C 964 " --> pdb=" O MET C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 973 removed outlier: 3.569A pdb=" N ASN C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 Processing helix chain 'C' and resid 996 through 1019 removed outlier: 3.845A pdb=" N LEU C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1038 Processing helix chain 'C' and resid 1041 through 1087 removed outlier: 4.429A pdb=" N VAL C1045 " --> pdb=" O LEU C1041 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C1046 " --> pdb=" O GLU C1042 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C1074 " --> pdb=" O GLU C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1198 removed outlier: 3.574A pdb=" N SER C1198 " --> pdb=" O PRO C1195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 5.753A pdb=" N ASP A 92 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 83 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 94 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET A 81 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 80 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 198 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS A 289 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLU A 200 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.835A pdb=" N THR A 55 " --> pdb=" O TYR C 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.538A pdb=" N PHE A 67 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN A 311 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP A 327 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU A 313 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 325 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 315 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.630A pdb=" N ILE A 304 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 77 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 302 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 251 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 271 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 253 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 104 removed outlier: 4.580A pdb=" N ALA A 138 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 172 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 229 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA A 174 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A 227 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR A 176 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N CYS A 225 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 147 removed outlier: 4.009A pdb=" N ARG A 155 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.850A pdb=" N PHE A 355 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AB1, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.641A pdb=" N GLU A 370 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 396 " --> pdb=" O CYS A 572 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.621A pdb=" N SER A 389 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 411 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 472 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 409 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 490 through 496 removed outlier: 6.020A pdb=" N GLY A 541 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS A 495 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR A 539 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG A 542 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP A 527 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 595 through 596 Processing sheet with id=AB5, first strand: chain 'A' and resid 604 through 607 removed outlier: 3.810A pdb=" N GLY A 628 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 619 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 55 " --> pdb=" O PHE A 618 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 705 through 710 removed outlier: 3.875A pdb=" N THR A 706 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL A 740 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP A 708 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 737 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 747 through 748 removed outlier: 6.039A pdb=" N LEU A 747 " --> pdb=" O SER B 837 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 756 through 765 removed outlier: 6.709A pdb=" N ASP A1125 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE A 765 " --> pdb=" O PRO A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.706A pdb=" N VAL A1104 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AC2, first strand: chain 'A' and resid 836 through 837 Processing sheet with id=AC3, first strand: chain 'A' and resid 1177 through 1180 removed outlier: 4.245A pdb=" N CYS A1143 " --> pdb=" O VAL A1180 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS A1136 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1149 through 1153 Processing sheet with id=AC5, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.588A pdb=" N LEU B 63 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 75 through 78 removed outlier: 7.025A pdb=" N LEU B 253 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.648A pdb=" N THR B 160 " --> pdb=" O CYS B 177 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 172 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 229 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 174 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 227 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYR B 176 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N CYS B 225 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 178 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 223 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 120 through 122 removed outlier: 4.447A pdb=" N ALA B 298 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 133 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.922A pdb=" N ARG B 155 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.418A pdb=" N LEU B 198 " --> pdb=" O SER B 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.545A pdb=" N VAL B 649 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.526A pdb=" N GLU B 370 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 396 " --> pdb=" O CYS B 572 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 389 through 393 removed outlier: 3.760A pdb=" N SER B 389 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B 466 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS B 414 " --> pdb=" O THR B 466 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG B 468 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE B 412 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS B 470 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 490 through 496 removed outlier: 5.967A pdb=" N GLY B 541 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS B 495 " --> pdb=" O TYR B 539 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR B 539 " --> pdb=" O CYS B 495 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG B 542 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP B 527 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 595 through 596 Processing sheet with id=AD7, first strand: chain 'B' and resid 604 through 607 Processing sheet with id=AD8, first strand: chain 'B' and resid 626 through 629 removed outlier: 6.343A pdb=" N VAL B 619 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 704 through 709 removed outlier: 7.055A pdb=" N HIS B 704 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL B 740 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N THR B 706 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 737 " --> pdb=" O LYS B 724 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 747 through 748 removed outlier: 5.954A pdb=" N LEU B 747 " --> pdb=" O SER C 837 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 756 through 765 removed outlier: 6.364A pdb=" N ASP B1125 " --> pdb=" O THR B 763 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE B 765 " --> pdb=" O PRO B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 769 through 774 removed outlier: 3.729A pdb=" N VAL B1104 " --> pdb=" O VAL B1119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AE5, first strand: chain 'B' and resid 1177 through 1180 removed outlier: 4.284A pdb=" N CYS B1143 " --> pdb=" O VAL B1180 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS B1136 " --> pdb=" O LEU B1189 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1149 through 1153 Processing sheet with id=AE7, first strand: chain 'C' and resid 26 through 27 removed outlier: 6.580A pdb=" N ASP C 26 " --> pdb=" O ILE C 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 60 through 67 removed outlier: 7.543A pdb=" N ASN C 311 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP C 327 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU C 313 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA C 325 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU C 315 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.420A pdb=" N ALA C 301 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 114 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 303 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 251 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 271 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 253 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.444A pdb=" N SER C 80 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU C 198 " --> pdb=" O SER C 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.666A pdb=" N LYS C 229 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.754A pdb=" N LYS C 133 " --> pdb=" O ALA C 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 145 through 147 removed outlier: 4.046A pdb=" N ARG C 155 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.819A pdb=" N VAL C 178 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AF7, first strand: chain 'C' and resid 370 through 371 removed outlier: 6.544A pdb=" N GLU C 370 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.860A pdb=" N SER C 389 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 490 through 496 removed outlier: 6.004A pdb=" N GLY C 541 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS C 495 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR C 539 " --> pdb=" O CYS C 495 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG C 542 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP C 527 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 595 through 596 Processing sheet with id=AG2, first strand: chain 'C' and resid 604 through 606 removed outlier: 3.618A pdb=" N ALA C 640 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 693 through 694 Processing sheet with id=AG4, first strand: chain 'C' and resid 704 through 705 removed outlier: 6.858A pdb=" N HIS C 704 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N VAL C 740 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 737 " --> pdb=" O LYS C 724 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 756 through 759 Processing sheet with id=AG6, first strand: chain 'C' and resid 762 through 765 removed outlier: 6.768A pdb=" N ASP C1125 " --> pdb=" O THR C 763 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE C 765 " --> pdb=" O PRO C1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 769 through 774 removed outlier: 3.638A pdb=" N VAL C1104 " --> pdb=" O VAL C1119 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 781 through 783 Processing sheet with id=AG9, first strand: chain 'C' and resid 1135 through 1136 removed outlier: 3.801A pdb=" N CYS C1136 " --> pdb=" O GLN C1187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'C' and resid 1143 through 1146 removed outlier: 4.306A pdb=" N CYS C1143 " --> pdb=" O VAL C1180 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1150 through 1153 944 hydrogen bonds defined for protein. 2556 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: 5.56 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8589 1.35 - 1.48: 7223 1.48 - 1.61: 11345 1.61 - 1.75: 0 1.75 - 1.88: 243 Bond restraints: 27400 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.577 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" CB ASN C 118 " pdb=" CG ASN C 118 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.48e+00 bond pdb=" CA ASP B1004 " pdb=" C ASP B1004 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 4.99e+00 bond pdb=" CB CYS C 177 " pdb=" SG CYS C 177 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.48e+00 bond pdb=" CA TYR C 100 " pdb=" C TYR C 100 " ideal model delta sigma weight residual 1.522 1.496 0.025 1.31e-02 5.83e+03 3.78e+00 ... (remaining 27395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 36794 3.00 - 6.00: 323 6.00 - 8.99: 42 8.99 - 11.99: 5 11.99 - 14.99: 2 Bond angle restraints: 37166 Sorted by residual: angle pdb=" N TYR C 100 " pdb=" CA TYR C 100 " pdb=" C TYR C 100 " ideal model delta sigma weight residual 113.89 103.17 10.72 1.58e+00 4.01e-01 4.61e+01 angle pdb=" N FOL B1407 " pdb=" CA FOL B1407 " pdb=" CB FOL B1407 " ideal model delta sigma weight residual 110.00 124.99 -14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" N FOL C1408 " pdb=" CA FOL C1408 " pdb=" CB FOL C1408 " ideal model delta sigma weight residual 110.00 124.87 -14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C LYS A 671 " pdb=" N MET A 672 " pdb=" CA MET A 672 " ideal model delta sigma weight residual 121.52 112.52 9.00 1.84e+00 2.95e-01 2.39e+01 angle pdb=" N ASP B1004 " pdb=" CA ASP B1004 " pdb=" C ASP B1004 " ideal model delta sigma weight residual 111.03 106.01 5.02 1.11e+00 8.12e-01 2.04e+01 ... (remaining 37161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 15276 21.98 - 43.96: 1350 43.96 - 65.95: 225 65.95 - 87.93: 108 87.93 - 109.91: 30 Dihedral angle restraints: 16989 sinusoidal: 7254 harmonic: 9735 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 3.37 -89.37 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A 372 " pdb=" SG CYS A 372 " pdb=" SG CYS A 396 " pdb=" CB CYS A 396 " ideal model delta sinusoidal sigma weight residual -86.00 -173.02 87.02 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " pdb=" SG CYS A 642 " pdb=" CB CYS A 642 " ideal model delta sinusoidal sigma weight residual -86.00 -154.93 68.93 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 16986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4204 0.149 - 0.297: 25 0.297 - 0.446: 3 0.446 - 0.594: 1 0.594 - 0.743: 3 Chirality restraints: 4236 Sorted by residual: chirality pdb=" CA FOL B1407 " pdb=" N FOL B1407 " pdb=" CB FOL B1407 " pdb=" CT FOL B1407 " both_signs ideal model delta sigma weight residual False -2.46 -1.72 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA FOL C1408 " pdb=" N FOL C1408 " pdb=" CB FOL C1408 " pdb=" CT FOL C1408 " both_signs ideal model delta sigma weight residual False -2.46 -1.77 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 399 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.96e+00 ... (remaining 4233 not shown) Planarity restraints: 4786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C1148 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ASN C1148 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN C1148 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY C1149 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 572 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO A 573 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 464 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 465 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " 0.036 5.00e-02 4.00e+02 ... (remaining 4783 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4098 2.76 - 3.30: 23870 3.30 - 3.83: 43786 3.83 - 4.37: 49194 4.37 - 4.90: 88094 Nonbonded interactions: 209042 Sorted by model distance: nonbonded pdb=" O ALA C 115 " pdb=" OG SER C 300 " model vdw 2.225 3.040 nonbonded pdb=" O GLU C 566 " pdb=" OH TYR C 620 " model vdw 2.253 3.040 nonbonded pdb=" O GLU B 566 " pdb=" OH TYR B 620 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASN A 487 " pdb=" ND2 ASN A 488 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR B 803 " pdb=" OD1 ASN B1052 " model vdw 2.287 3.040 ... (remaining 209037 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 22 through 1406 or resid 1409)) selection = (chain 'B' and (resid 22 through 1406 or resid 1409)) selection = (chain 'C' and (resid 22 through 1406 or resid 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27495 Z= 0.206 Angle : 0.761 14.989 37400 Z= 0.373 Chirality : 0.053 0.743 4236 Planarity : 0.005 0.073 4754 Dihedral : 17.724 109.910 10617 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.52 % Allowed : 20.73 % Favored : 78.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.14), residues: 3264 helix: -0.19 (0.17), residues: 747 sheet: -0.31 (0.20), residues: 687 loop : -1.26 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.027 0.002 TYR B 594 PHE 0.022 0.002 PHE C 355 TRP 0.028 0.002 TRP B 299 HIS 0.008 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00445 (27400) covalent geometry : angle 0.73542 (37166) SS BOND : bond 0.00582 ( 48) SS BOND : angle 1.45213 ( 96) hydrogen bonds : bond 0.20866 ( 940) hydrogen bonds : angle 7.51628 ( 2556) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00845 ( 14) link_BETA1-4 : angle 2.74731 ( 42) link_NAG-ASN : bond 0.00522 ( 32) link_NAG-ASN : angle 3.33384 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8780 (mt) cc_final: 0.8522 (tt) REVERT: C 31 TYR cc_start: 0.6501 (m-80) cc_final: 0.6219 (m-80) outliers start: 15 outliers final: 9 residues processed: 179 average time/residue: 0.1367 time to fit residues: 42.6175 Evaluate side-chains 173 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 907 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 ASN A1174 ASN ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 805 GLN C1191 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081761 restraints weight = 58228.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084022 restraints weight = 34301.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085554 restraints weight = 24090.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.086553 restraints weight = 18945.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087263 restraints weight = 16119.607| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27495 Z= 0.227 Angle : 0.648 10.948 37400 Z= 0.322 Chirality : 0.045 0.386 4236 Planarity : 0.004 0.057 4754 Dihedral : 10.252 86.402 4665 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.21 % Allowed : 18.48 % Favored : 78.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.14), residues: 3264 helix: 0.60 (0.19), residues: 762 sheet: -0.43 (0.19), residues: 738 loop : -1.06 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 867 TYR 0.016 0.001 TYR B 594 PHE 0.018 0.002 PHE A 355 TRP 0.014 0.001 TRP A 434 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00520 (27400) covalent geometry : angle 0.62297 (37166) SS BOND : bond 0.00472 ( 48) SS BOND : angle 1.24535 ( 96) hydrogen bonds : bond 0.04638 ( 940) hydrogen bonds : angle 5.56506 ( 2556) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00797 ( 14) link_BETA1-4 : angle 2.89010 ( 42) link_NAG-ASN : bond 0.00355 ( 32) link_NAG-ASN : angle 2.82622 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 169 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: A 672 MET cc_start: 0.7588 (pmm) cc_final: 0.7224 (pmm) REVERT: A 889 TYR cc_start: 0.6648 (t80) cc_final: 0.6418 (t80) REVERT: A 923 MET cc_start: 0.8841 (tpt) cc_final: 0.8587 (tpt) REVERT: B 27 MET cc_start: 0.7165 (ttt) cc_final: 0.6926 (ttt) REVERT: B 814 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8660 (mm) REVERT: C 31 TYR cc_start: 0.6586 (m-80) cc_final: 0.6231 (m-80) REVERT: C 1175 PHE cc_start: 0.7821 (m-80) cc_final: 0.7599 (m-10) outliers start: 93 outliers final: 55 residues processed: 247 average time/residue: 0.1316 time to fit residues: 56.5974 Evaluate side-chains 213 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1056 THR Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 221 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS B 486 ASN B 821 GLN B1140 ASN C 265 ASN C1191 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081920 restraints weight = 57755.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084185 restraints weight = 34110.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085722 restraints weight = 23966.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086748 restraints weight = 18847.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087428 restraints weight = 16021.920| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27495 Z= 0.170 Angle : 0.600 11.854 37400 Z= 0.295 Chirality : 0.043 0.367 4236 Planarity : 0.004 0.053 4754 Dihedral : 8.671 87.069 4654 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.21 % Allowed : 19.24 % Favored : 77.55 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3264 helix: 0.92 (0.19), residues: 765 sheet: -0.52 (0.19), residues: 702 loop : -0.95 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 867 TYR 0.016 0.001 TYR B 594 PHE 0.021 0.001 PHE C 355 TRP 0.012 0.001 TRP A 434 HIS 0.004 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00389 (27400) covalent geometry : angle 0.57539 (37166) SS BOND : bond 0.00397 ( 48) SS BOND : angle 1.32140 ( 96) hydrogen bonds : bond 0.04259 ( 940) hydrogen bonds : angle 5.22128 ( 2556) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00831 ( 14) link_BETA1-4 : angle 2.70028 ( 42) link_NAG-ASN : bond 0.00312 ( 32) link_NAG-ASN : angle 2.67451 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 162 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: A 672 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6302 (ptp) REVERT: A 923 MET cc_start: 0.8832 (tpt) cc_final: 0.8550 (tpt) REVERT: B 27 MET cc_start: 0.7177 (ttt) cc_final: 0.6961 (ttt) REVERT: B 312 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8646 (m-10) REVERT: B 592 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7292 (mm) REVERT: B 814 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8674 (mm) REVERT: C 31 TYR cc_start: 0.6446 (m-80) cc_final: 0.6039 (m-80) REVERT: C 669 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.6661 (t-90) REVERT: C 672 MET cc_start: 0.7279 (ptm) cc_final: 0.6901 (ptp) outliers start: 93 outliers final: 66 residues processed: 242 average time/residue: 0.1241 time to fit residues: 52.4021 Evaluate side-chains 225 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 153 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 892 CYS Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1141 THR Chi-restraints excluded: chain C residue 1143 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 66 optimal weight: 0.0070 chunk 126 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 188 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 overall best weight: 0.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS B 486 ASN B1129 GLN C 183 ASN C 190 HIS C 356 ASN C1191 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084469 restraints weight = 57326.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086782 restraints weight = 33757.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088333 restraints weight = 23644.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089369 restraints weight = 18550.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089933 restraints weight = 15732.696| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27495 Z= 0.095 Angle : 0.534 11.314 37400 Z= 0.263 Chirality : 0.042 0.321 4236 Planarity : 0.003 0.049 4754 Dihedral : 7.327 88.693 4654 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.59 % Allowed : 19.00 % Favored : 77.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3264 helix: 1.48 (0.20), residues: 747 sheet: -0.39 (0.20), residues: 675 loop : -0.89 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 286 TYR 0.014 0.001 TYR B 594 PHE 0.014 0.001 PHE B 355 TRP 0.010 0.001 TRP A 434 HIS 0.003 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00203 (27400) covalent geometry : angle 0.51405 (37166) SS BOND : bond 0.00330 ( 48) SS BOND : angle 0.83685 ( 96) hydrogen bonds : bond 0.03572 ( 940) hydrogen bonds : angle 4.85903 ( 2556) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00818 ( 14) link_BETA1-4 : angle 2.39802 ( 42) link_NAG-ASN : bond 0.00366 ( 32) link_NAG-ASN : angle 2.38706 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 169 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: A 672 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6281 (ptp) REVERT: A 923 MET cc_start: 0.8829 (tpt) cc_final: 0.8508 (tpt) REVERT: A 985 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6507 (tt) REVERT: B 62 MET cc_start: 0.7795 (tmm) cc_final: 0.7580 (tmm) REVERT: B 337 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: B 556 MET cc_start: 0.8105 (mtp) cc_final: 0.7618 (ttm) REVERT: B 639 MET cc_start: 0.7511 (mtm) cc_final: 0.7271 (mtm) REVERT: B 814 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 239 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: C 669 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6691 (t-90) outliers start: 104 outliers final: 64 residues processed: 258 average time/residue: 0.1358 time to fit residues: 60.8099 Evaluate side-chains 232 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Chi-restraints excluded: chain C residue 1143 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 296 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A1192 ASN ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN B1084 ASN C 190 HIS C1191 ASN C1192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080418 restraints weight = 57866.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082632 restraints weight = 34172.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084141 restraints weight = 24002.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085056 restraints weight = 18928.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085784 restraints weight = 16245.460| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27495 Z= 0.245 Angle : 0.645 12.413 37400 Z= 0.318 Chirality : 0.045 0.356 4236 Planarity : 0.004 0.052 4754 Dihedral : 7.436 88.091 4654 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.49 % Allowed : 19.00 % Favored : 76.51 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 3264 helix: 0.86 (0.19), residues: 783 sheet: -0.49 (0.20), residues: 693 loop : -0.99 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 867 TYR 0.019 0.002 TYR B 594 PHE 0.019 0.002 PHE B 355 TRP 0.014 0.001 TRP A 434 HIS 0.007 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00570 (27400) covalent geometry : angle 0.62124 (37166) SS BOND : bond 0.00531 ( 48) SS BOND : angle 1.44202 ( 96) hydrogen bonds : bond 0.04320 ( 940) hydrogen bonds : angle 5.03328 ( 2556) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00662 ( 14) link_BETA1-4 : angle 2.69356 ( 42) link_NAG-ASN : bond 0.00328 ( 32) link_NAG-ASN : angle 2.68489 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 160 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8770 (mt-10) REVERT: A 672 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6426 (ptp) REVERT: B 62 MET cc_start: 0.7820 (tmm) cc_final: 0.7498 (tmm) REVERT: B 312 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8704 (m-10) REVERT: B 587 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7406 (pp) REVERT: B 814 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8617 (mm) REVERT: C 1066 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8192 (mp) outliers start: 130 outliers final: 101 residues processed: 272 average time/residue: 0.1379 time to fit residues: 64.7837 Evaluate side-chains 263 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 156 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1056 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 204 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 0.3980 chunk 199 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN C 190 HIS C1191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081882 restraints weight = 57826.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084174 restraints weight = 34013.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085714 restraints weight = 23788.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086724 restraints weight = 18654.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087213 restraints weight = 15851.102| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27495 Z= 0.144 Angle : 0.571 11.957 37400 Z= 0.280 Chirality : 0.043 0.333 4236 Planarity : 0.003 0.051 4754 Dihedral : 7.065 88.149 4654 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.11 % Allowed : 19.62 % Favored : 76.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3264 helix: 1.04 (0.19), residues: 783 sheet: -0.44 (0.20), residues: 693 loop : -0.93 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 324 TYR 0.017 0.001 TYR B 594 PHE 0.016 0.001 PHE B 355 TRP 0.011 0.001 TRP A 434 HIS 0.003 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00330 (27400) covalent geometry : angle 0.54960 (37166) SS BOND : bond 0.00413 ( 48) SS BOND : angle 1.15813 ( 96) hydrogen bonds : bond 0.03849 ( 940) hydrogen bonds : angle 4.85762 ( 2556) Misc. bond : bond 0.00041 ( 1) link_BETA1-4 : bond 0.00721 ( 14) link_BETA1-4 : angle 2.36576 ( 42) link_NAG-ASN : bond 0.00286 ( 32) link_NAG-ASN : angle 2.50569 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 164 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: A 566 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8706 (mt-10) REVERT: A 672 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6495 (ptp) REVERT: B 27 MET cc_start: 0.7145 (ttt) cc_final: 0.6933 (ttt) REVERT: B 62 MET cc_start: 0.7798 (tmm) cc_final: 0.7437 (tmm) REVERT: B 587 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7322 (pp) REVERT: B 592 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7263 (mm) REVERT: B 814 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8697 (mm) outliers start: 119 outliers final: 92 residues processed: 264 average time/residue: 0.1227 time to fit residues: 56.4250 Evaluate side-chains 256 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 158 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Chi-restraints excluded: chain C residue 1143 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 chunk 166 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081695 restraints weight = 57517.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083944 restraints weight = 33828.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085472 restraints weight = 23743.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.086487 restraints weight = 18650.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087176 restraints weight = 15850.454| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27495 Z= 0.156 Angle : 0.575 11.967 37400 Z= 0.283 Chirality : 0.043 0.334 4236 Planarity : 0.004 0.050 4754 Dihedral : 6.926 88.147 4654 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.46 % Allowed : 19.93 % Favored : 75.61 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.15), residues: 3264 helix: 1.07 (0.19), residues: 783 sheet: -0.44 (0.20), residues: 693 loop : -0.93 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 324 TYR 0.017 0.001 TYR B 594 PHE 0.017 0.001 PHE B 355 TRP 0.011 0.001 TRP A 434 HIS 0.004 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00361 (27400) covalent geometry : angle 0.55476 (37166) SS BOND : bond 0.00425 ( 48) SS BOND : angle 1.10487 ( 96) hydrogen bonds : bond 0.03848 ( 940) hydrogen bonds : angle 4.81600 ( 2556) Misc. bond : bond 0.00027 ( 1) link_BETA1-4 : bond 0.00657 ( 14) link_BETA1-4 : angle 2.32497 ( 42) link_NAG-ASN : bond 0.00277 ( 32) link_NAG-ASN : angle 2.49744 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 163 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: A 555 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: A 566 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (mt-10) REVERT: A 672 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6786 (ptp) REVERT: B 27 MET cc_start: 0.6938 (ttt) cc_final: 0.6680 (ttt) REVERT: B 587 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7312 (pp) REVERT: B 592 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7274 (mm) REVERT: B 814 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8682 (mm) REVERT: C 694 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: C 1066 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8163 (mp) outliers start: 129 outliers final: 102 residues processed: 274 average time/residue: 0.1241 time to fit residues: 58.5581 Evaluate side-chains 271 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 160 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 694 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Chi-restraints excluded: chain C residue 1143 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 294 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 322 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN B 486 ASN C 356 ASN C1191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082387 restraints weight = 57785.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084671 restraints weight = 33859.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086220 restraints weight = 23697.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087170 restraints weight = 18585.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087901 restraints weight = 15875.994| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27495 Z= 0.134 Angle : 0.562 11.858 37400 Z= 0.275 Chirality : 0.042 0.331 4236 Planarity : 0.003 0.047 4754 Dihedral : 6.692 89.012 4654 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.15 % Allowed : 20.45 % Favored : 75.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3264 helix: 1.16 (0.20), residues: 783 sheet: -0.47 (0.20), residues: 699 loop : -0.88 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.015 0.001 TYR B 594 PHE 0.018 0.001 PHE C 355 TRP 0.011 0.001 TRP A 434 HIS 0.003 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00306 (27400) covalent geometry : angle 0.54356 (37166) SS BOND : bond 0.00386 ( 48) SS BOND : angle 0.97451 ( 96) hydrogen bonds : bond 0.03682 ( 940) hydrogen bonds : angle 4.72398 ( 2556) Misc. bond : bond 0.00037 ( 1) link_BETA1-4 : bond 0.00722 ( 14) link_BETA1-4 : angle 2.17763 ( 42) link_NAG-ASN : bond 0.00287 ( 32) link_NAG-ASN : angle 2.41513 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 169 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6697 (m-80) REVERT: A 442 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8756 (ptpt) REVERT: A 555 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: A 566 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: A 672 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6755 (ptp) REVERT: B 27 MET cc_start: 0.6967 (ttt) cc_final: 0.6738 (ttt) REVERT: B 587 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7300 (pp) REVERT: B 592 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7252 (mm) REVERT: B 814 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8697 (mm) REVERT: C 110 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9015 (m) REVERT: C 694 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: C 1066 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8078 (mp) outliers start: 120 outliers final: 96 residues processed: 271 average time/residue: 0.1292 time to fit residues: 60.6941 Evaluate side-chains 267 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 160 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 694 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Chi-restraints excluded: chain C residue 1143 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 293 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080554 restraints weight = 58133.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082808 restraints weight = 34434.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084300 restraints weight = 24169.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085312 restraints weight = 19043.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085983 restraints weight = 16222.060| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27495 Z= 0.211 Angle : 0.621 11.926 37400 Z= 0.305 Chirality : 0.044 0.336 4236 Planarity : 0.004 0.048 4754 Dihedral : 6.886 87.834 4654 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.42 % Allowed : 20.17 % Favored : 75.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 3264 helix: 1.07 (0.19), residues: 765 sheet: -0.52 (0.20), residues: 714 loop : -0.95 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 468 TYR 0.023 0.001 TYR C 889 PHE 0.019 0.001 PHE C 355 TRP 0.013 0.001 TRP A 434 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00489 (27400) covalent geometry : angle 0.60072 (37166) SS BOND : bond 0.00495 ( 48) SS BOND : angle 1.24982 ( 96) hydrogen bonds : bond 0.04078 ( 940) hydrogen bonds : angle 4.86048 ( 2556) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00614 ( 14) link_BETA1-4 : angle 2.28548 ( 42) link_NAG-ASN : bond 0.00295 ( 32) link_NAG-ASN : angle 2.55068 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 164 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: A 442 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8704 (ptpt) REVERT: A 555 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: A 566 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8757 (mt-10) REVERT: B 27 MET cc_start: 0.7191 (ttt) cc_final: 0.6954 (ttt) REVERT: B 62 MET cc_start: 0.7710 (tmm) cc_final: 0.7356 (tmm) REVERT: B 312 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8736 (m-10) REVERT: B 587 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7260 (pp) REVERT: B 592 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 720 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 814 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8629 (mm) REVERT: C 110 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (m) REVERT: C 694 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7180 (tp40) REVERT: C 1066 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8188 (mp) outliers start: 128 outliers final: 100 residues processed: 274 average time/residue: 0.1373 time to fit residues: 64.9048 Evaluate side-chains 274 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 162 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 694 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 49 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 239 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081832 restraints weight = 57677.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084120 restraints weight = 33923.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085651 restraints weight = 23672.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086669 restraints weight = 18650.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087278 restraints weight = 15822.539| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27495 Z= 0.146 Angle : 0.582 11.798 37400 Z= 0.286 Chirality : 0.043 0.322 4236 Planarity : 0.003 0.048 4754 Dihedral : 6.717 87.751 4654 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.87 % Allowed : 20.86 % Favored : 75.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 3264 helix: 1.21 (0.20), residues: 765 sheet: -0.53 (0.20), residues: 738 loop : -0.91 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.027 0.001 TYR C 889 PHE 0.023 0.001 PHE C 355 TRP 0.011 0.001 TRP A 434 HIS 0.003 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00338 (27400) covalent geometry : angle 0.56294 (37166) SS BOND : bond 0.00465 ( 48) SS BOND : angle 1.23008 ( 96) hydrogen bonds : bond 0.03757 ( 940) hydrogen bonds : angle 4.75647 ( 2556) Misc. bond : bond 0.00039 ( 1) link_BETA1-4 : bond 0.00693 ( 14) link_BETA1-4 : angle 2.11366 ( 42) link_NAG-ASN : bond 0.00281 ( 32) link_NAG-ASN : angle 2.44459 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 164 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: A 345 MET cc_start: 0.7919 (mmm) cc_final: 0.7579 (mmt) REVERT: A 442 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8707 (ptpt) REVERT: A 555 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: A 566 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8712 (mt-10) REVERT: B 27 MET cc_start: 0.7062 (ttt) cc_final: 0.6843 (ttt) REVERT: B 62 MET cc_start: 0.7644 (tmm) cc_final: 0.7399 (tmm) REVERT: B 335 GLN cc_start: 0.8290 (mt0) cc_final: 0.7950 (mt0) REVERT: B 587 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7236 (pp) REVERT: B 592 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7306 (mm) REVERT: B 814 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8687 (mm) REVERT: B 1066 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 110 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9021 (m) REVERT: C 694 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7161 (tp40) REVERT: C 1066 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8115 (mp) outliers start: 112 outliers final: 97 residues processed: 260 average time/residue: 0.1419 time to fit residues: 63.1305 Evaluate side-chains 269 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 161 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 669 HIS Chi-restraints excluded: chain C residue 694 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1083 VAL Chi-restraints excluded: chain C residue 1086 CYS Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 147 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082382 restraints weight = 57648.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084674 restraints weight = 33999.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086196 restraints weight = 23780.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087208 restraints weight = 18715.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087825 restraints weight = 15894.812| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27495 Z= 0.130 Angle : 0.566 11.021 37400 Z= 0.278 Chirality : 0.042 0.326 4236 Planarity : 0.003 0.048 4754 Dihedral : 6.518 88.555 4654 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.01 % Allowed : 20.62 % Favored : 75.37 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.15), residues: 3264 helix: 1.30 (0.20), residues: 765 sheet: -0.50 (0.20), residues: 699 loop : -0.87 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.026 0.001 TYR C 889 PHE 0.022 0.001 PHE C 355 TRP 0.010 0.001 TRP A 434 HIS 0.003 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00298 (27400) covalent geometry : angle 0.54714 (37166) SS BOND : bond 0.00422 ( 48) SS BOND : angle 1.12982 ( 96) hydrogen bonds : bond 0.03623 ( 940) hydrogen bonds : angle 4.67770 ( 2556) Misc. bond : bond 0.00042 ( 1) link_BETA1-4 : bond 0.00693 ( 14) link_BETA1-4 : angle 2.05459 ( 42) link_NAG-ASN : bond 0.00282 ( 32) link_NAG-ASN : angle 2.36542 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.58 seconds wall clock time: 56 minutes 14.27 seconds (3374.27 seconds total)