Starting phenix.real_space_refine on Fri Sep 19 11:12:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmp_61609/09_2025/9jmp_61609.cif" } resolution = 3.1 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= 0.007 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 150 5.16 5 C 16086 2.51 5 N 4137 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25407 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8228 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1014} Chain breaks: 8 Chain: "B" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8228 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1014} Chain breaks: 7 Chain: "C" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8228 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1014} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 118 Unusual residues: {'EIC': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 118 Unusual residues: {'EIC': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 118 Unusual residues: {'EIC': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.81, per 1000 atoms: 0.23 Number of scatterers: 25407 At special positions: 0 Unit cell: (158.4, 151.8, 142.56, 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 150 16.00 O 5034 8.00 N 4137 7.00 C 16086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 624 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS A 718 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 824 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 813 " distance=2.03 Simple disulfide: pdb=" SG CYS A 908 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A1102 " - pdb=" SG CYS A1113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 607 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 624 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 683 " - pdb=" SG CYS B 718 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 824 " distance=2.03 Simple disulfide: pdb=" SG CYS B 807 " - pdb=" SG CYS B 813 " distance=2.03 Simple disulfide: pdb=" SG CYS B 908 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B1102 " - pdb=" SG CYS B1113 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 353 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 482 " distance=2.04 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 506 " - pdb=" SG CYS C 530 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 624 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 683 " - pdb=" SG CYS C 718 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 824 " distance=2.03 Simple disulfide: pdb=" SG CYS C 807 " - pdb=" SG CYS C 813 " distance=2.04 Simple disulfide: pdb=" SG CYS C 908 " - pdb=" SG CYS C 921 " distance=2.03 Simple disulfide: pdb=" SG CYS C1102 " - pdb=" SG CYS C1113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1401 " - " ASN A 159 " " NAG A1402 " - " ASN A 52 " " NAG A1403 " - " ASN A 248 " " NAG A1404 " - " ASN A 724 " " NAG A1405 " - " ASN A 866 " " NAG A1406 " - " ASN A 623 " " NAG A1407 " - " ASN A 170 " " NAG B1401 " - " ASN B 52 " " NAG B1402 " - " ASN B 159 " " NAG B1403 " - " ASN B 724 " " NAG B1404 " - " ASN B 866 " " NAG B1405 " - " ASN B 170 " " NAG B1406 " - " ASN B 623 " " NAG B1407 " - " ASN B 248 " " NAG C1402 " - " ASN C 724 " " NAG C1403 " - " ASN C 866 " " NAG C1404 " - " ASN C 170 " " NAG C1405 " - " ASN C 248 " " NAG C1406 " - " ASN C 623 " " NAG C1407 " - " ASN C 159 " " NAG C1408 " - " ASN C 52 " " NAG D 1 " - " ASN A 69 " " NAG E 1 " - " ASN A 130 " " NAG F 1 " - " ASN A 226 " " NAG G 1 " - " ASN A 414 " " NAG H 1 " - " ASN B 130 " " NAG I 1 " - " ASN B 226 " " NAG J 1 " - " ASN B 414 " " NAG K 1 " - " ASN B 69 " " NAG L 1 " - " ASN C 69 " " NAG M 1 " - " ASN C 130 " " NAG N 1 " - " ASN C 414 " " NAG O 1 " - " ASN C 226 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 51 sheets defined 27.2% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.632A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.659A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.665A pdb=" N LYS A 457 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER A 458 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.615A pdb=" N GLN A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.806A pdb=" N ASN A 532 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 533 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.510A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 801 through 808 Processing helix chain 'A' and resid 810 through 818 removed outlier: 3.692A pdb=" N LEU A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 848 removed outlier: 3.602A pdb=" N CYS A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 Processing helix chain 'A' and resid 903 through 910 Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.953A pdb=" N TYR A 924 " --> pdb=" O CYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.644A pdb=" N ILE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.543A pdb=" N LEU A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1003 through 1009 removed outlier: 3.554A pdb=" N THR A1006 " --> pdb=" O ALA A1003 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1008 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A1009 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1035 removed outlier: 3.624A pdb=" N SER A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1046 through 1052 Processing helix chain 'A' and resid 1055 through 1103 removed outlier: 3.967A pdb=" N ALA A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.503A pdb=" N GLU B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.506A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.633A pdb=" N GLN B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.755A pdb=" N LYS B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 532 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 533 " --> pdb=" O CYS B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 528 through 533' Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.088A pdb=" N LEU B 604 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 688 removed outlier: 3.582A pdb=" N ILE B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 808 Processing helix chain 'B' and resid 810 through 818 Processing helix chain 'B' and resid 820 through 847 Processing helix chain 'B' and resid 884 through 893 Processing helix chain 'B' and resid 903 through 911 Processing helix chain 'B' and resid 919 through 927 removed outlier: 4.636A pdb=" N TYR B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 925 " --> pdb=" O CYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 950 removed outlier: 3.602A pdb=" N GLU B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 942 " --> pdb=" O ASN B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 979 removed outlier: 3.708A pdb=" N ILE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 989 removed outlier: 3.616A pdb=" N ASN B 989 " --> pdb=" O VAL B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1003 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.966A pdb=" N PHE B1008 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1035 removed outlier: 3.590A pdb=" N SER B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1046 through 1054 Processing helix chain 'B' and resid 1055 through 1103 removed outlier: 3.745A pdb=" N GLU B1060 " --> pdb=" O PRO B1056 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA B1061 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B1062 " --> pdb=" O GLU B1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.881A pdb=" N TYR C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.757A pdb=" N LEU C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 456 through 461 removed outlier: 3.567A pdb=" N GLN C 461 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.651A pdb=" N GLN C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.796A pdb=" N LYS C 531 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN C 532 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 533 " --> pdb=" O CYS C 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 528 through 533' Processing helix chain 'C' and resid 682 through 688 removed outlier: 3.580A pdb=" N ILE C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 806 Processing helix chain 'C' and resid 810 through 818 Processing helix chain 'C' and resid 820 through 846 Processing helix chain 'C' and resid 884 through 894 Processing helix chain 'C' and resid 903 through 910 removed outlier: 3.650A pdb=" N LYS C 910 " --> pdb=" O ASP C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 941 through 951 removed outlier: 3.895A pdb=" N ILE C 951 " --> pdb=" O LEU C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 978 removed outlier: 3.755A pdb=" N GLY C 978 " --> pdb=" O TYR C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 989 Processing helix chain 'C' and resid 989 through 1003 Processing helix chain 'C' and resid 1004 through 1006 No H-bonds generated for 'chain 'C' and resid 1004 through 1006' Processing helix chain 'C' and resid 1012 through 1035 removed outlier: 3.535A pdb=" N SER C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1029 " --> pdb=" O ASN C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1038 No H-bonds generated for 'chain 'C' and resid 1036 through 1038' Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1055 through 1103 removed outlier: 3.639A pdb=" N ALA C1061 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C1064 " --> pdb=" O GLU C1060 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.292A pdb=" N SER A 66 " --> pdb=" O TYR C 636 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 635 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE C 643 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE C 378 " --> pdb=" O ASN C 611 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 78 removed outlier: 4.353A pdb=" N ARG A 339 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.695A pdb=" N ASN A 263 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 267 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR A 287 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 269 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.640A pdb=" N ALA A 150 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.640A pdb=" N ALA A 150 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.862A pdb=" N ALA A 313 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.718A pdb=" N SER A 156 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 210 through 212 removed outlier: 5.853A pdb=" N VAL A 210 " --> pdb=" O SER A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AB2, first strand: chain 'A' and resid 377 through 380 removed outlier: 6.730A pdb=" N PHE A 378 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 643 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 635 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.094A pdb=" N VAL A 385 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS A 411 " --> pdb=" O CYS A 589 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 404 through 408 removed outlier: 7.085A pdb=" N THR A 481 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS A 429 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 485 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 516 through 519 removed outlier: 6.335A pdb=" N VAL A 561 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS A 506 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 559 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 508 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 557 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 543 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 723 through 729 removed outlier: 8.010A pdb=" N LEU A 755 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET A 727 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 784 through 792 removed outlier: 6.279A pdb=" N TYR A1137 " --> pdb=" O HIS A1118 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS A1118 " --> pdb=" O TYR A1137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AB9, first strand: chain 'A' and resid 861 through 862 removed outlier: 3.958A pdb=" N PHE A 865 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AC2, first strand: chain 'B' and resid 71 through 78 removed outlier: 4.364A pdb=" N ARG B 339 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 86 through 89 removed outlier: 3.601A pdb=" N ALA B 286 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B 271 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 284 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.674A pdb=" N ALA B 150 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.674A pdb=" N ALA B 150 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.974A pdb=" N ALA B 313 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.622A pdb=" N GLY B 166 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 210 through 212 removed outlier: 5.754A pdb=" N VAL B 210 " --> pdb=" O SER B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 363 through 365 removed outlier: 3.517A pdb=" N GLY B 717 " --> pdb=" O THR B 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.570A pdb=" N ILE B 643 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 635 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 385 through 386 removed outlier: 5.960A pdb=" N VAL B 385 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 411 " --> pdb=" O CYS B 589 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 404 through 408 removed outlier: 6.917A pdb=" N THR B 481 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N CYS B 429 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG B 483 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 427 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 485 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 517 through 519 removed outlier: 6.263A pdb=" N VAL B 561 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS B 506 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 559 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG B 508 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE B 557 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 723 through 729 removed outlier: 3.938A pdb=" N SER B 725 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 757 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET B 727 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 783 through 792 removed outlier: 3.547A pdb=" N VAL B1120 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B1137 " --> pdb=" O HIS B1118 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS B1118 " --> pdb=" O TYR B1137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 797 through 800 removed outlier: 4.719A pdb=" N LYS B 797 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AD9, first strand: chain 'C' and resid 33 through 36 Processing sheet with id=AE1, first strand: chain 'C' and resid 70 through 78 removed outlier: 4.531A pdb=" N ARG C 339 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.622A pdb=" N ALA C 286 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 271 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU C 284 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.674A pdb=" N ALA C 150 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.674A pdb=" N ALA C 150 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 132 through 134 removed outlier: 3.868A pdb=" N ALA C 313 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.495A pdb=" N SER C 156 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 210 through 212 removed outlier: 6.183A pdb=" N VAL C 210 " --> pdb=" O SER C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 363 through 365 removed outlier: 3.541A pdb=" N GLY C 717 " --> pdb=" O THR C 714 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 385 through 386 removed outlier: 6.124A pdb=" N VAL C 385 " --> pdb=" O ASN C 412 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.564A pdb=" N SER C 444 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.263A pdb=" N VAL C 561 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS C 506 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 559 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 508 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE C 557 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 728 through 729 removed outlier: 4.234A pdb=" N LEU C 734 " --> pdb=" O ALA C 742 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 781 through 792 removed outlier: 4.260A pdb=" N ASN C 781 " --> pdb=" O THR C1140 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR C1140 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 783 " --> pdb=" O VAL C1138 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C1137 " --> pdb=" O HIS C1118 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS C1118 " --> pdb=" O TYR C1137 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 798 through 800 Processing sheet with id=AF6, first strand: chain 'C' and resid 861 through 862 1061 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.49: 15151 1.49 - 1.77: 10608 1.77 - 2.05: 203 2.05 - 2.33: 0 2.33 - 2.61: 1 Bond restraints: 25963 Sorted by residual: bond pdb=" C ASN B 98 " pdb=" N TYR B 101 " ideal model delta sigma weight residual 1.330 2.608 -1.278 1.44e-02 4.82e+03 7.88e+03 bond pdb=" CA ASP C 602 " pdb=" C ASP C 602 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.37e-02 5.33e+03 2.30e+01 bond pdb=" CA SER B 95 " pdb=" C SER B 95 " ideal model delta sigma weight residual 1.530 1.484 0.047 1.08e-02 8.57e+03 1.88e+01 bond pdb=" N ASP C 96 " pdb=" CA ASP C 96 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" CA SER A 95 " pdb=" C SER A 95 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.23e-02 6.61e+03 8.73e+00 ... (remaining 25958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.20: 35239 12.20 - 24.41: 1 24.41 - 36.61: 0 36.61 - 48.81: 0 48.81 - 61.02: 1 Bond angle restraints: 35241 Sorted by residual: angle pdb=" O ASN B 98 " pdb=" C ASN B 98 " pdb=" N TYR B 101 " ideal model delta sigma weight residual 122.59 61.57 61.02 1.33e+00 5.65e-01 2.10e+03 angle pdb=" C ASN B 98 " pdb=" N TYR B 101 " pdb=" CA TYR B 101 " ideal model delta sigma weight residual 122.94 142.01 -19.07 1.50e+00 4.44e-01 1.62e+02 angle pdb=" CA ASN B 98 " pdb=" C ASN B 98 " pdb=" N TYR B 101 " ideal model delta sigma weight residual 116.84 107.69 9.15 1.71e+00 3.42e-01 2.86e+01 angle pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" C ASP B 96 " ideal model delta sigma weight residual 111.28 116.25 -4.97 1.09e+00 8.42e-01 2.08e+01 angle pdb=" CA GLU C 41 " pdb=" CB GLU C 41 " pdb=" CG GLU C 41 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.57e+01 ... (remaining 35236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 14610 21.90 - 43.81: 1205 43.81 - 65.71: 188 65.71 - 87.62: 76 87.62 - 109.52: 17 Dihedral angle restraints: 16096 sinusoidal: 6849 harmonic: 9247 Sorted by residual: dihedral pdb=" CB CYS C 343 " pdb=" SG CYS C 343 " pdb=" SG CYS C 353 " pdb=" CB CYS C 353 " ideal model delta sinusoidal sigma weight residual 93.00 174.85 -81.85 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 908 " pdb=" SG CYS A 908 " pdb=" SG CYS A 921 " pdb=" CB CYS A 921 " ideal model delta sinusoidal sigma weight residual -86.00 -165.73 79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS C 732 " pdb=" SG CYS C 732 " pdb=" SG CYS C 741 " pdb=" CB CYS C 741 " ideal model delta sinusoidal sigma weight residual -86.00 -151.11 65.11 1 1.00e+01 1.00e-02 5.56e+01 ... (remaining 16093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3229 0.055 - 0.109: 688 0.109 - 0.164: 127 0.164 - 0.219: 5 0.219 - 0.273: 4 Chirality restraints: 4053 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG B1406 " pdb=" ND2 ASN B 623 " pdb=" C2 NAG B1406 " pdb=" O5 NAG B1406 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4050 not shown) Planarity restraints: 4552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 98 " 0.188 2.00e-02 2.50e+03 2.76e-01 7.63e+02 pdb=" C ASN B 98 " -0.447 2.00e-02 2.50e+03 pdb=" O ASN B 98 " 0.265 2.00e-02 2.50e+03 pdb=" N TYR B 101 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1008 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C PHE A1008 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A1008 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A1009 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1126 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO A1127 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " 0.037 5.00e-02 4.00e+02 ... (remaining 4549 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6508 2.80 - 3.32: 21069 3.32 - 3.85: 42458 3.85 - 4.37: 50104 4.37 - 4.90: 87020 Nonbonded interactions: 207159 Sorted by model distance: nonbonded pdb=" OH TYR A 413 " pdb=" OH TYR A 442 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 413 " pdb=" OH TYR B 442 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR C 413 " pdb=" OH TYR C 442 " model vdw 2.290 3.040 nonbonded pdb=" OD2 ASP C 448 " pdb=" OH TYR C 473 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU B 380 " pdb=" OH TYR B 645 " model vdw 2.303 3.040 ... (remaining 207154 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 1140 or resid 1402 through 1407)) selection = (chain 'B' and (resid 18 through 1140 or resid 1402 through 1407)) selection = (chain 'C' and (resid 18 through 1140 or resid 1402 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.530 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.009 1.278 26059 Z= 0.587 Angle : 0.757 61.017 35481 Z= 0.429 Chirality : 0.047 0.273 4053 Planarity : 0.007 0.276 4519 Dihedral : 16.526 109.523 10054 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.29 % Allowed : 18.35 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3141 helix: -0.13 (0.17), residues: 747 sheet: 0.49 (0.20), residues: 705 loop : -0.97 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 818 TYR 0.037 0.001 TYR C 205 PHE 0.024 0.002 PHE A 211 TRP 0.031 0.001 TRP A 47 HIS 0.013 0.001 HIS C 852 Details of bonding type rmsd covalent geometry : bond 0.00899 (25963) covalent geometry : angle 0.74163 (35241) SS BOND : bond 0.00258 ( 48) SS BOND : angle 1.16802 ( 96) hydrogen bonds : bond 0.18722 ( 1004) hydrogen bonds : angle 7.69190 ( 2910) link_BETA1-4 : bond 0.00485 ( 15) link_BETA1-4 : angle 1.65686 ( 45) link_NAG-ASN : bond 0.00390 ( 33) link_NAG-ASN : angle 2.66494 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 691 HIS cc_start: 0.4858 (t70) cc_final: 0.4630 (t-90) REVERT: C 212 ASP cc_start: 0.6997 (t0) cc_final: 0.6299 (t0) outliers start: 8 outliers final: 5 residues processed: 170 average time/residue: 0.1676 time to fit residues: 45.8929 Evaluate side-chains 163 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 1034 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 698 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.082514 restraints weight = 35759.633| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.94 r_work: 0.2762 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26059 Z= 0.130 Angle : 0.536 8.290 35481 Z= 0.281 Chirality : 0.043 0.269 4053 Planarity : 0.004 0.057 4519 Dihedral : 8.338 77.083 4490 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 16.50 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3143 helix: 0.95 (0.19), residues: 750 sheet: 0.63 (0.19), residues: 741 loop : -0.86 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 818 TYR 0.013 0.001 TYR B1137 PHE 0.014 0.001 PHE C 121 TRP 0.015 0.001 TRP A 47 HIS 0.004 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00289 (25963) covalent geometry : angle 0.52018 (35241) SS BOND : bond 0.00229 ( 48) SS BOND : angle 0.87661 ( 96) hydrogen bonds : bond 0.04741 ( 1004) hydrogen bonds : angle 5.77162 ( 2910) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.79984 ( 45) link_NAG-ASN : bond 0.00225 ( 33) link_NAG-ASN : angle 2.10760 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 632 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7933 (mm110) REVERT: A 814 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 884 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 517 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: B 689 MET cc_start: 0.6491 (ptm) cc_final: 0.6240 (ptp) REVERT: C 212 ASP cc_start: 0.7202 (t0) cc_final: 0.6458 (t0) REVERT: C 375 ARG cc_start: 0.6840 (mmt90) cc_final: 0.6513 (mmt-90) REVERT: C 551 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7172 (mm-40) REVERT: C 632 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7385 (mm110) REVERT: C 889 LEU cc_start: 0.8641 (tp) cc_final: 0.8420 (tt) outliers start: 52 outliers final: 29 residues processed: 202 average time/residue: 0.1579 time to fit residues: 52.2911 Evaluate side-chains 189 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 861 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 1 optimal weight: 8.9990 chunk 176 optimal weight: 0.0570 chunk 69 optimal weight: 8.9990 chunk 166 optimal weight: 0.0770 chunk 170 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN B 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.082676 restraints weight = 35864.434| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.03 r_work: 0.2763 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26059 Z= 0.140 Angle : 0.529 7.984 35481 Z= 0.273 Chirality : 0.043 0.249 4053 Planarity : 0.004 0.059 4519 Dihedral : 6.750 58.246 4487 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.47 % Allowed : 15.85 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3143 helix: 1.33 (0.20), residues: 735 sheet: 0.56 (0.19), residues: 732 loop : -0.78 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 338 TYR 0.019 0.001 TYR A 198 PHE 0.014 0.001 PHE C 117 TRP 0.016 0.001 TRP A 47 HIS 0.006 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00326 (25963) covalent geometry : angle 0.51197 (35241) SS BOND : bond 0.00239 ( 48) SS BOND : angle 0.96070 ( 96) hydrogen bonds : bond 0.04338 ( 1004) hydrogen bonds : angle 5.27544 ( 2910) link_BETA1-4 : bond 0.00255 ( 15) link_BETA1-4 : angle 1.94105 ( 45) link_NAG-ASN : bond 0.00261 ( 33) link_NAG-ASN : angle 2.05060 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7403 (m-80) cc_final: 0.7196 (m-80) REVERT: A 415 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 517 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: A 632 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: A 884 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8867 (p) REVERT: A 947 LEU cc_start: 0.8839 (mt) cc_final: 0.8605 (mt) REVERT: B 295 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8770 (mttm) REVERT: B 517 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: B 576 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 689 MET cc_start: 0.6581 (ptm) cc_final: 0.6335 (ptp) REVERT: C 35 MET cc_start: 0.8564 (tpp) cc_final: 0.8325 (ttp) REVERT: C 41 GLU cc_start: 0.6830 (pp20) cc_final: 0.6598 (pp20) REVERT: C 212 ASP cc_start: 0.7242 (t0) cc_final: 0.6551 (t0) REVERT: C 302 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7340 (ttp-170) REVERT: C 632 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7330 (mm110) REVERT: C 743 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8917 (t) REVERT: C 943 TYR cc_start: 0.7479 (m-80) cc_final: 0.7264 (m-80) outliers start: 68 outliers final: 40 residues processed: 229 average time/residue: 0.1529 time to fit residues: 56.9306 Evaluate side-chains 206 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1113 CYS Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 127 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 81 optimal weight: 0.1980 chunk 238 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.082633 restraints weight = 35785.526| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.08 r_work: 0.2734 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26059 Z= 0.134 Angle : 0.511 8.033 35481 Z= 0.265 Chirality : 0.043 0.241 4053 Planarity : 0.004 0.057 4519 Dihedral : 6.074 58.416 4487 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.79 % Allowed : 15.67 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.15), residues: 3143 helix: 1.49 (0.20), residues: 735 sheet: 0.54 (0.18), residues: 750 loop : -0.79 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 338 TYR 0.019 0.001 TYR A 198 PHE 0.013 0.001 PHE C 117 TRP 0.017 0.001 TRP A 47 HIS 0.007 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00312 (25963) covalent geometry : angle 0.49457 (35241) SS BOND : bond 0.00253 ( 48) SS BOND : angle 0.96209 ( 96) hydrogen bonds : bond 0.04146 ( 1004) hydrogen bonds : angle 5.12346 ( 2910) link_BETA1-4 : bond 0.00290 ( 15) link_BETA1-4 : angle 1.82869 ( 45) link_NAG-ASN : bond 0.00242 ( 33) link_NAG-ASN : angle 2.02226 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 165 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: A 632 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7866 (mm110) REVERT: A 884 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8849 (p) REVERT: A 947 LEU cc_start: 0.8831 (mt) cc_final: 0.8591 (mt) REVERT: B 371 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6630 (pm20) REVERT: B 517 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: C 35 MET cc_start: 0.8665 (tpp) cc_final: 0.8457 (ttp) REVERT: C 41 GLU cc_start: 0.6883 (pp20) cc_final: 0.6662 (pp20) REVERT: C 212 ASP cc_start: 0.7218 (t0) cc_final: 0.6786 (t0) REVERT: C 229 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8229 (tt) REVERT: C 302 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7363 (ttp-170) REVERT: C 375 ARG cc_start: 0.6828 (mmt90) cc_final: 0.6608 (mmt-90) REVERT: C 576 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9173 (mm) REVERT: C 632 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7348 (mm110) REVERT: C 743 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8945 (t) REVERT: C 1138 VAL cc_start: 0.8807 (m) cc_final: 0.8601 (p) outliers start: 77 outliers final: 44 residues processed: 229 average time/residue: 0.1545 time to fit residues: 58.5613 Evaluate side-chains 212 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 861 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 144 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 692 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.081518 restraints weight = 35825.150| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.82 r_work: 0.2727 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26059 Z= 0.180 Angle : 0.547 8.487 35481 Z= 0.283 Chirality : 0.044 0.246 4053 Planarity : 0.004 0.057 4519 Dihedral : 6.097 59.533 4487 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.01 % Allowed : 15.74 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 3143 helix: 1.44 (0.20), residues: 735 sheet: 0.48 (0.18), residues: 756 loop : -0.81 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 483 TYR 0.018 0.002 TYR A 198 PHE 0.019 0.001 PHE C 117 TRP 0.019 0.001 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00428 (25963) covalent geometry : angle 0.53065 (35241) SS BOND : bond 0.00292 ( 48) SS BOND : angle 1.04555 ( 96) hydrogen bonds : bond 0.04462 ( 1004) hydrogen bonds : angle 5.15711 ( 2910) link_BETA1-4 : bond 0.00250 ( 15) link_BETA1-4 : angle 1.88932 ( 45) link_NAG-ASN : bond 0.00324 ( 33) link_NAG-ASN : angle 2.11560 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 168 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: A 632 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8008 (mm110) REVERT: A 884 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8860 (p) REVERT: A 947 LEU cc_start: 0.8842 (mt) cc_final: 0.8609 (mt) REVERT: B 238 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8976 (mt) REVERT: B 295 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8777 (mttm) REVERT: B 371 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: B 517 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7173 (tp30) REVERT: B 576 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9153 (mm) REVERT: C 41 GLU cc_start: 0.6867 (pp20) cc_final: 0.6628 (pp20) REVERT: C 212 ASP cc_start: 0.7223 (t0) cc_final: 0.6843 (t0) REVERT: C 302 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7356 (ttp-170) REVERT: C 375 ARG cc_start: 0.7005 (mmt90) cc_final: 0.6780 (mmt-90) REVERT: C 576 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9192 (mm) REVERT: C 632 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7406 (mm110) REVERT: C 733 GLN cc_start: 0.7979 (mm110) cc_final: 0.7692 (mp10) REVERT: C 943 TYR cc_start: 0.7500 (m-80) cc_final: 0.7172 (m-80) outliers start: 83 outliers final: 52 residues processed: 235 average time/residue: 0.1546 time to fit residues: 59.4175 Evaluate side-chains 224 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.081531 restraints weight = 35830.980| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.99 r_work: 0.2723 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26059 Z= 0.135 Angle : 0.510 7.919 35481 Z= 0.264 Chirality : 0.043 0.238 4053 Planarity : 0.004 0.056 4519 Dihedral : 5.930 58.295 4487 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.58 % Allowed : 16.43 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.15), residues: 3143 helix: 1.53 (0.20), residues: 735 sheet: 0.53 (0.18), residues: 750 loop : -0.79 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 483 TYR 0.016 0.001 TYR A 198 PHE 0.013 0.001 PHE C 117 TRP 0.018 0.001 TRP A 47 HIS 0.007 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00315 (25963) covalent geometry : angle 0.49410 (35241) SS BOND : bond 0.00248 ( 48) SS BOND : angle 0.89272 ( 96) hydrogen bonds : bond 0.04111 ( 1004) hydrogen bonds : angle 5.03886 ( 2910) link_BETA1-4 : bond 0.00224 ( 15) link_BETA1-4 : angle 1.72470 ( 45) link_NAG-ASN : bond 0.00255 ( 33) link_NAG-ASN : angle 2.01005 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 632 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8027 (mm110) REVERT: A 884 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 925 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8778 (m) REVERT: A 947 LEU cc_start: 0.8805 (mt) cc_final: 0.8577 (mt) REVERT: A 1137 TYR cc_start: 0.7590 (t80) cc_final: 0.7030 (t80) REVERT: B 238 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8965 (mt) REVERT: B 371 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: B 517 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: B 576 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9136 (mm) REVERT: C 41 GLU cc_start: 0.6838 (pp20) cc_final: 0.6593 (pp20) REVERT: C 212 ASP cc_start: 0.7224 (t0) cc_final: 0.6875 (t0) REVERT: C 229 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 302 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6670 (ttp-170) REVERT: C 326 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8794 (m) REVERT: C 375 ARG cc_start: 0.6917 (mmt90) cc_final: 0.6698 (mmt-90) REVERT: C 576 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9148 (mm) REVERT: C 733 GLN cc_start: 0.7975 (mm110) cc_final: 0.7682 (mp10) outliers start: 71 outliers final: 48 residues processed: 226 average time/residue: 0.1490 time to fit residues: 55.5280 Evaluate side-chains 223 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 984 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.079096 restraints weight = 35927.437| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.94 r_work: 0.2621 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26059 Z= 0.209 Angle : 0.572 8.636 35481 Z= 0.294 Chirality : 0.045 0.251 4053 Planarity : 0.004 0.057 4519 Dihedral : 6.209 59.677 4487 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.87 % Allowed : 16.39 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.15), residues: 3143 helix: 1.36 (0.20), residues: 729 sheet: 0.31 (0.18), residues: 759 loop : -0.78 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 483 TYR 0.016 0.002 TYR A 198 PHE 0.020 0.002 PHE C 117 TRP 0.021 0.002 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00501 (25963) covalent geometry : angle 0.55463 (35241) SS BOND : bond 0.00322 ( 48) SS BOND : angle 1.13199 ( 96) hydrogen bonds : bond 0.04650 ( 1004) hydrogen bonds : angle 5.19191 ( 2910) link_BETA1-4 : bond 0.00186 ( 15) link_BETA1-4 : angle 1.94188 ( 45) link_NAG-ASN : bond 0.00368 ( 33) link_NAG-ASN : angle 2.17783 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 167 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7536 (t0) cc_final: 0.7276 (t0) REVERT: A 632 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8014 (mm110) REVERT: A 884 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 925 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 947 LEU cc_start: 0.8845 (mt) cc_final: 0.8621 (mt) REVERT: A 1137 TYR cc_start: 0.7670 (t80) cc_final: 0.7095 (t80) REVERT: B 238 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8984 (mt) REVERT: B 295 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (mttm) REVERT: B 371 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6516 (pm20) REVERT: B 517 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: B 576 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9157 (mm) REVERT: C 41 GLU cc_start: 0.7011 (pp20) cc_final: 0.6758 (pp20) REVERT: C 212 ASP cc_start: 0.7306 (t0) cc_final: 0.6899 (t0) REVERT: C 302 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7402 (ttp-170) REVERT: C 326 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (m) REVERT: C 576 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9218 (mm) REVERT: C 632 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7450 (mm110) REVERT: C 733 GLN cc_start: 0.8082 (mm110) cc_final: 0.7814 (mp10) REVERT: C 943 TYR cc_start: 0.7431 (m-80) cc_final: 0.7165 (m-80) outliers start: 79 outliers final: 51 residues processed: 233 average time/residue: 0.1537 time to fit residues: 58.4614 Evaluate side-chains 227 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 256 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN C 984 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.080883 restraints weight = 35882.116| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.91 r_work: 0.2717 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26059 Z= 0.137 Angle : 0.516 7.931 35481 Z= 0.267 Chirality : 0.043 0.241 4053 Planarity : 0.004 0.056 4519 Dihedral : 5.963 59.711 4487 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.47 % Allowed : 16.94 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 3143 helix: 1.51 (0.20), residues: 735 sheet: 0.41 (0.18), residues: 780 loop : -0.75 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.014 0.001 TYR A 198 PHE 0.013 0.001 PHE C 117 TRP 0.019 0.001 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00321 (25963) covalent geometry : angle 0.50017 (35241) SS BOND : bond 0.00253 ( 48) SS BOND : angle 0.92348 ( 96) hydrogen bonds : bond 0.04140 ( 1004) hydrogen bonds : angle 5.04408 ( 2910) link_BETA1-4 : bond 0.00227 ( 15) link_BETA1-4 : angle 1.72606 ( 45) link_NAG-ASN : bond 0.00264 ( 33) link_NAG-ASN : angle 2.03850 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7455 (t0) cc_final: 0.7177 (t0) REVERT: A 884 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 925 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 947 LEU cc_start: 0.8815 (mt) cc_final: 0.8585 (mt) REVERT: A 1137 TYR cc_start: 0.7606 (t80) cc_final: 0.7146 (t80) REVERT: B 238 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8963 (mt) REVERT: B 371 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: B 517 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: B 576 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9130 (mm) REVERT: C 41 GLU cc_start: 0.6957 (pp20) cc_final: 0.6713 (pp20) REVERT: C 212 ASP cc_start: 0.7255 (t0) cc_final: 0.6921 (t0) REVERT: C 229 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8279 (tt) REVERT: C 302 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.6252 (ttp-170) REVERT: C 576 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9183 (mm) REVERT: C 733 GLN cc_start: 0.8057 (mm110) cc_final: 0.7809 (mp10) outliers start: 68 outliers final: 48 residues processed: 229 average time/residue: 0.1479 time to fit residues: 56.0244 Evaluate side-chains 225 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 20 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN C 632 GLN C 984 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.081612 restraints weight = 35719.850| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.95 r_work: 0.2735 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26059 Z= 0.114 Angle : 0.499 7.814 35481 Z= 0.259 Chirality : 0.042 0.232 4053 Planarity : 0.004 0.056 4519 Dihedral : 5.728 59.722 4487 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.10 % Allowed : 17.48 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.15), residues: 3143 helix: 1.57 (0.20), residues: 735 sheet: 0.53 (0.18), residues: 750 loop : -0.74 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.013 0.001 TYR A 198 PHE 0.013 0.001 PHE B 782 TRP 0.016 0.001 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00262 (25963) covalent geometry : angle 0.48429 (35241) SS BOND : bond 0.00219 ( 48) SS BOND : angle 0.88472 ( 96) hydrogen bonds : bond 0.03919 ( 1004) hydrogen bonds : angle 4.94042 ( 2910) link_BETA1-4 : bond 0.00258 ( 15) link_BETA1-4 : angle 1.63944 ( 45) link_NAG-ASN : bond 0.00234 ( 33) link_NAG-ASN : angle 1.93153 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.833 Fit side-chains REVERT: A 212 ASP cc_start: 0.7452 (t0) cc_final: 0.7197 (t0) REVERT: A 884 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 925 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8796 (m) REVERT: A 947 LEU cc_start: 0.8746 (mt) cc_final: 0.8521 (mt) REVERT: A 1137 TYR cc_start: 0.7567 (t80) cc_final: 0.7136 (t80) REVERT: B 238 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8974 (mt) REVERT: B 371 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: B 517 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: B 576 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9113 (mm) REVERT: C 41 GLU cc_start: 0.6941 (pp20) cc_final: 0.6699 (pp20) REVERT: C 180 CYS cc_start: 0.7647 (m) cc_final: 0.7443 (m) REVERT: C 212 ASP cc_start: 0.7326 (t0) cc_final: 0.6982 (t0) REVERT: C 302 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6209 (ttp-170) REVERT: C 375 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6869 (mmt-90) REVERT: C 576 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9167 (mm) REVERT: C 733 GLN cc_start: 0.8040 (mm110) cc_final: 0.7807 (mp10) REVERT: C 943 TYR cc_start: 0.7354 (m-80) cc_final: 0.7108 (m-80) outliers start: 58 outliers final: 43 residues processed: 216 average time/residue: 0.1442 time to fit residues: 51.4767 Evaluate side-chains 215 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 91 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 314 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN C 984 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.080779 restraints weight = 35804.101| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.95 r_work: 0.2712 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26059 Z= 0.148 Angle : 0.521 7.895 35481 Z= 0.269 Chirality : 0.043 0.239 4053 Planarity : 0.004 0.055 4519 Dihedral : 5.806 59.896 4486 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.29 % Allowed : 17.30 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.15), residues: 3143 helix: 1.54 (0.20), residues: 735 sheet: 0.45 (0.18), residues: 780 loop : -0.70 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 483 TYR 0.015 0.001 TYR B 205 PHE 0.014 0.001 PHE C 117 TRP 0.018 0.001 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00349 (25963) covalent geometry : angle 0.50549 (35241) SS BOND : bond 0.00260 ( 48) SS BOND : angle 0.97156 ( 96) hydrogen bonds : bond 0.04143 ( 1004) hydrogen bonds : angle 4.98317 ( 2910) link_BETA1-4 : bond 0.00200 ( 15) link_BETA1-4 : angle 1.72898 ( 45) link_NAG-ASN : bond 0.00266 ( 33) link_NAG-ASN : angle 1.98110 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.826 Fit side-chains REVERT: A 632 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8042 (mm110) REVERT: A 884 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 925 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (m) REVERT: A 947 LEU cc_start: 0.8813 (mt) cc_final: 0.8605 (mt) REVERT: A 1137 TYR cc_start: 0.7637 (t80) cc_final: 0.7263 (t80) REVERT: B 238 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8963 (mt) REVERT: B 371 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: B 517 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: B 576 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9124 (mm) REVERT: C 41 GLU cc_start: 0.6977 (pp20) cc_final: 0.6736 (pp20) REVERT: C 180 CYS cc_start: 0.7650 (m) cc_final: 0.7438 (m) REVERT: C 212 ASP cc_start: 0.7354 (t0) cc_final: 0.7014 (t0) REVERT: C 302 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.6680 (ttp-170) REVERT: C 576 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9202 (mm) REVERT: C 838 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8294 (tt0) outliers start: 63 outliers final: 47 residues processed: 219 average time/residue: 0.1523 time to fit residues: 55.0777 Evaluate side-chains 223 residues out of total 2757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 1011 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 249 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN C 984 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.080634 restraints weight = 35620.905| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.96 r_work: 0.2712 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26059 Z= 0.147 Angle : 0.523 7.910 35481 Z= 0.270 Chirality : 0.043 0.239 4053 Planarity : 0.004 0.055 4519 Dihedral : 5.811 58.719 4486 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.25 % Allowed : 17.30 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 3143 helix: 1.60 (0.20), residues: 717 sheet: 0.45 (0.17), residues: 810 loop : -0.76 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 483 TYR 0.015 0.001 TYR A 198 PHE 0.013 0.001 PHE C 117 TRP 0.018 0.001 TRP A 47 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00348 (25963) covalent geometry : angle 0.50835 (35241) SS BOND : bond 0.00262 ( 48) SS BOND : angle 0.95409 ( 96) hydrogen bonds : bond 0.04141 ( 1004) hydrogen bonds : angle 4.99177 ( 2910) link_BETA1-4 : bond 0.00203 ( 15) link_BETA1-4 : angle 1.71506 ( 45) link_NAG-ASN : bond 0.00269 ( 33) link_NAG-ASN : angle 1.99986 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5539.91 seconds wall clock time: 95 minutes 53.27 seconds (5753.27 seconds total)