Starting phenix.real_space_refine on Tue Jun 24 23:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.map" model { file = "/net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ato_43831/06_2025/9ato_43831.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 17661 2.51 5 N 4582 2.21 5 O 5354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 1.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27725 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8152 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 57, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8188 Classifications: {'peptide': 1046} Link IDs: {'PTRANS': 57, 'TRANS': 988} Chain breaks: 7 Chain: "C" Number of atoms: 8188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8188 Classifications: {'peptide': 1046} Link IDs: {'PTRANS': 57, 'TRANS': 988} Chain breaks: 7 Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "F" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} 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: 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 17.78, per 1000 atoms: 0.64 Number of scatterers: 27725 At special positions: 0 Unit cell: (145.195, 150.507, 208.053, 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 128 16.00 O 5354 8.00 N 4582 7.00 C 17661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.04 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 278 " " NAG A1302 " - " ASN A 327 " " NAG A1303 " - " ASN A 705 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 327 " " NAG B1303 " - " ASN B 705 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 278 " " NAG C1303 " - " ASN C 327 " " NAG C1304 " - " ASN C 705 " " NAG G 1 " - " ASN A 713 " " NAG H 1 " - " ASN A 797 " " NAG I 1 " - " ASN A1070 " " NAG J 1 " - " ASN A1094 " " NAG K 1 " - " ASN A1130 " " NAG M 1 " - " ASN B 713 " " NAG N 1 " - " ASN B 797 " " NAG O 1 " - " ASN B1070 " " NAG P 1 " - " ASN B1094 " " NAG Q 1 " - " ASN B1130 " " NAG S 1 " - " ASN C 713 " " NAG T 1 " - " ASN C 797 " " NAG U 1 " - " ASN C1070 " " NAG V 1 " - " ASN C1094 " " NAG W 1 " - " ASN C1130 " Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.7 seconds 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6506 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 23.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.136A pdb=" N ILE A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.964A pdb=" N ASN A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 612 through 616 removed outlier: 4.037A pdb=" N VAL A 616 " --> pdb=" O CYS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.662A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.572A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.658A pdb=" N ILE A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.061A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 removed outlier: 3.962A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 3.865A pdb=" N GLN A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1143 removed outlier: 4.220A pdb=" N GLU A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 333 through 339 removed outlier: 4.152A pdb=" N VAL B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.588A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.925A pdb=" N PHE B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.846A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.068A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 612 through 616 removed outlier: 4.006A pdb=" N VAL B 616 " --> pdb=" O CYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.816A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.678A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 821 Processing helix chain 'B' and resid 846 through 851 Processing helix chain 'B' and resid 862 through 881 removed outlier: 3.622A pdb=" N GLY B 881 " --> pdb=" O THR B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 905 removed outlier: 3.561A pdb=" N ILE B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 3.519A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 removed outlier: 3.792A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 937 " --> pdb=" O SER B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.566A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 3.915A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1143 removed outlier: 4.389A pdb=" N GLU B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.237A pdb=" N ILE C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.622A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 434 through 439 Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.902A pdb=" N VAL C 616 " --> pdb=" O CYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.661A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.544A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.747A pdb=" N ILE C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.244A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 Processing helix chain 'C' and resid 941 through 961 Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.632A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.276A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'L' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 27 removed outlier: 7.726A pdb=" N ASN A 58 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A 265 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.653A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 4.047A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 4.235A pdb=" N GLY A 100 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 164 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.247A pdb=" N LEU A 138 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 315 removed outlier: 6.913A pdb=" N VAL A 591 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN A 313 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 589 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 324 removed outlier: 5.239A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 562 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE A 561 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.519A pdb=" N ALA A 372 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 7.031A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.651A pdb=" N TYR A 485 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.005A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 698 removed outlier: 6.838A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.420A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.420A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 732 Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AB9, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AC1, first strand: chain 'B' and resid 19 through 27 removed outlier: 8.123A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 52 removed outlier: 4.156A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.511A pdb=" N VAL B 123 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 166 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 125 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 164 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL B 127 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N CYS B 162 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 158 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 138 through 140 removed outlier: 6.185A pdb=" N LEU B 138 " --> pdb=" O LEU B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 307 through 315 removed outlier: 7.063A pdb=" N VAL B 591 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B 313 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY B 589 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 324 removed outlier: 5.583A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 562 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 561 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 350 through 354 removed outlier: 3.892A pdb=" N VAL B 391 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 removed outlier: 5.963A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 697 through 699 Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.603A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.603A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 729 through 731 removed outlier: 4.587A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AD6, first strand: chain 'C' and resid 20 through 27 removed outlier: 3.577A pdb=" N THR C 60 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 90 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 88 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 191 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 52 removed outlier: 4.124A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.679A pdb=" N VAL C 117 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 164 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 138 through 140 removed outlier: 6.296A pdb=" N LEU C 138 " --> pdb=" O LEU C 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 307 through 315 removed outlier: 6.769A pdb=" N VAL C 591 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN C 313 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 589 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AE3, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.808A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AE5, first strand: chain 'C' and resid 469 through 470 removed outlier: 3.584A pdb=" N TYR C 485 " --> pdb=" O TYR C 469 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.062A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.596A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 730 through 732 Processing sheet with id=AE9, first strand: chain 'C' and resid 1116 through 1118 Processing sheet with id=AF1, first strand: chain 'C' and resid 1090 through 1093 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.343A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET D 34 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 2 through 7 removed outlier: 3.644A pdb=" N THR F 68 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.075A pdb=" N GLY F 10 " --> pdb=" O THR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.500A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 97 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.312A pdb=" N GLY L 10 " --> pdb=" O THR L 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.601A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET L 34 " --> pdb=" O PHE L 50 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA L 97 " --> pdb=" O TYR L 104 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3084 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: 15.84 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8772 1.34 - 1.46: 6894 1.46 - 1.59: 12528 1.59 - 1.71: 0 1.71 - 1.84: 164 Bond restraints: 28358 Sorted by residual: bond pdb=" N PHE F 29 " pdb=" CA PHE F 29 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.19e+01 bond pdb=" N PHE B 325 " pdb=" CA PHE B 325 " ideal model delta sigma weight residual 1.455 1.485 -0.029 7.00e-03 2.04e+04 1.77e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.10e+01 bond pdb=" N ILE B 328 " pdb=" CA ILE B 328 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.19e-02 7.06e+03 9.96e+00 ... (remaining 28353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 38123 2.54 - 5.07: 418 5.07 - 7.61: 25 7.61 - 10.15: 8 10.15 - 12.69: 3 Bond angle restraints: 38577 Sorted by residual: angle pdb=" CA ILE F 28 " pdb=" C ILE F 28 " pdb=" O ILE F 28 " ideal model delta sigma weight residual 121.68 117.65 4.03 7.90e-01 1.60e+00 2.60e+01 angle pdb=" C ASN B1130 " pdb=" N ASN B1131 " pdb=" CA ASN B1131 " ideal model delta sigma weight residual 122.73 131.78 -9.05 1.92e+00 2.71e-01 2.22e+01 angle pdb=" N ASN B1130 " pdb=" CA ASN B1130 " pdb=" C ASN B1130 " ideal model delta sigma weight residual 108.02 116.23 -8.21 1.75e+00 3.27e-01 2.20e+01 angle pdb=" CA LYS D 75 " pdb=" CB LYS D 75 " pdb=" CG LYS D 75 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" N THR B 329 " pdb=" CA THR B 329 " pdb=" C THR B 329 " ideal model delta sigma weight residual 114.31 109.30 5.01 1.29e+00 6.01e-01 1.51e+01 ... (remaining 38572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 16123 24.02 - 48.04: 1132 48.04 - 72.06: 142 72.06 - 96.08: 34 96.08 - 120.10: 3 Dihedral angle restraints: 17434 sinusoidal: 7321 harmonic: 10113 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 95 " pdb=" CB CYS F 95 " ideal model delta sinusoidal sigma weight residual 93.00 174.37 -81.37 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " pdb=" SG CYS A 297 " pdb=" CB CYS A 297 " ideal model delta sinusoidal sigma weight residual -86.00 -155.08 69.08 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS B 332 " pdb=" SG CYS B 332 " pdb=" SG CYS B 357 " pdb=" CB CYS B 357 " ideal model delta sinusoidal sigma weight residual 93.00 34.44 58.56 1 1.00e+01 1.00e-02 4.59e+01 ... (remaining 17431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 4463 0.179 - 0.357: 10 0.357 - 0.536: 3 0.536 - 0.714: 0 0.714 - 0.893: 1 Chirality restraints: 4477 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B1130 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 278 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 705 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.71e+00 ... (remaining 4474 not shown) Planarity restraints: 4958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1130 " 0.053 2.00e-02 2.50e+03 4.99e-02 3.12e+01 pdb=" CG ASN B1130 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B1130 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1130 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1130 " 0.001 2.00e-02 2.50e+03 4.11e-02 2.11e+01 pdb=" CG ASN A1130 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A1130 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A1130 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 705 " -0.035 2.00e-02 2.50e+03 3.30e-02 1.36e+01 pdb=" CG ASN B 705 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 705 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 705 " 0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.037 2.00e-02 2.50e+03 ... (remaining 4955 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1512 2.73 - 3.27: 26774 3.27 - 3.81: 44848 3.81 - 4.36: 52370 4.36 - 4.90: 92758 Nonbonded interactions: 218262 Sorted by model distance: nonbonded pdb=" OD2 ASP B 211 " pdb=" OH TYR B 262 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR B 319 " pdb=" OE1 GLU B 320 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 34 " pdb=" OD2 ASP B 50 " model vdw 2.209 3.040 nonbonded pdb=" NE2 GLN C 800 " pdb=" OE1 GLN C 931 " model vdw 2.215 3.120 nonbonded pdb=" OG SER L 52 " pdb=" OG SER L 56 " model vdw 2.228 3.040 ... (remaining 218257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 823 or resid 850 through 1143 or resid 1301 thr \ ough 1303)) selection = (chain 'C' and (resid 14 through 823 or resid 850 through 1143 or resid 1301 thr \ ough 1303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 68.940 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28443 Z= 0.190 Angle : 0.676 17.936 38787 Z= 0.344 Chirality : 0.050 0.893 4477 Planarity : 0.004 0.066 4933 Dihedral : 15.570 120.095 10793 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 0.36 % Allowed : 19.06 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3424 helix: 2.49 (0.21), residues: 670 sheet: 0.58 (0.16), residues: 916 loop : -0.64 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 101 HIS 0.003 0.001 HIS F 79 PHE 0.027 0.001 PHE B 370 TYR 0.024 0.001 TYR C 25 ARG 0.005 0.000 ARG L 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01211 ( 25) link_NAG-ASN : angle 5.56056 ( 75) link_BETA1-4 : bond 0.00790 ( 15) link_BETA1-4 : angle 1.99114 ( 45) hydrogen bonds : bond 0.12854 ( 1117) hydrogen bonds : angle 6.42208 ( 3084) SS BOND : bond 0.00260 ( 45) SS BOND : angle 1.26453 ( 90) covalent geometry : bond 0.00352 (28358) covalent geometry : angle 0.62558 (38577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.9001 (m-80) cc_final: 0.8777 (m-10) REVERT: C 432 TRP cc_start: 0.3359 (p90) cc_final: 0.2385 (p90) REVERT: F 36 TRP cc_start: 0.7394 (m100) cc_final: 0.7097 (m100) REVERT: F 94 TYR cc_start: 0.6454 (m-80) cc_final: 0.6055 (m-80) outliers start: 11 outliers final: 4 residues processed: 159 average time/residue: 0.3663 time to fit residues: 98.6884 Evaluate side-chains 142 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain D residue 83 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 270 optimal weight: 0.2980 chunk 104 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN B 953 GLN F 32 ASN F 44 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082019 restraints weight = 58494.243| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.94 r_work: 0.2961 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28443 Z= 0.127 Angle : 0.590 13.754 38787 Z= 0.294 Chirality : 0.046 0.510 4477 Planarity : 0.004 0.046 4933 Dihedral : 7.065 104.592 4575 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 1.78 % Allowed : 18.04 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3424 helix: 2.55 (0.20), residues: 656 sheet: 0.64 (0.16), residues: 928 loop : -0.63 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.007 0.001 HIS F 79 PHE 0.025 0.001 PHE B 370 TYR 0.019 0.001 TYR A1063 ARG 0.003 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 25) link_NAG-ASN : angle 4.22193 ( 75) link_BETA1-4 : bond 0.00505 ( 15) link_BETA1-4 : angle 1.08252 ( 45) hydrogen bonds : bond 0.04861 ( 1117) hydrogen bonds : angle 5.40905 ( 3084) SS BOND : bond 0.00219 ( 45) SS BOND : angle 1.02657 ( 90) covalent geometry : bond 0.00285 (28358) covalent geometry : angle 0.55810 (38577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: C 173 MET cc_start: 0.2502 (mmp) cc_final: 0.1130 (mtm) REVERT: C 432 TRP cc_start: 0.3150 (p90) cc_final: 0.2230 (p90) REVERT: F 34 MET cc_start: 0.7774 (mtm) cc_final: 0.7393 (mtm) REVERT: F 36 TRP cc_start: 0.8188 (m100) cc_final: 0.7612 (m100) REVERT: F 45 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7698 (ttp-170) outliers start: 54 outliers final: 19 residues processed: 188 average time/residue: 0.3454 time to fit residues: 111.7183 Evaluate side-chains 154 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 248 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN B 868 GLN B 998 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.141480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076406 restraints weight = 59237.782| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.42 r_work: 0.2780 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 28443 Z= 0.290 Angle : 0.676 17.559 38787 Z= 0.339 Chirality : 0.049 0.441 4477 Planarity : 0.004 0.046 4933 Dihedral : 6.845 102.954 4571 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.47 % Allowed : 18.14 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3424 helix: 2.12 (0.20), residues: 661 sheet: 0.49 (0.16), residues: 914 loop : -0.73 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 101 HIS 0.006 0.001 HIS A 950 PHE 0.022 0.002 PHE F 67 TYR 0.021 0.001 TYR A1063 ARG 0.009 0.000 ARG F 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 25) link_NAG-ASN : angle 4.40012 ( 75) link_BETA1-4 : bond 0.00237 ( 15) link_BETA1-4 : angle 1.24218 ( 45) hydrogen bonds : bond 0.06423 ( 1117) hydrogen bonds : angle 5.57268 ( 3084) SS BOND : bond 0.00303 ( 45) SS BOND : angle 1.21960 ( 90) covalent geometry : bond 0.00704 (28358) covalent geometry : angle 0.64498 (38577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 142 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: B 444 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7296 (m-40) REVERT: B 786 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8700 (ptpp) REVERT: C 49 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8448 (tm-30) REVERT: C 160 ASN cc_start: 0.7073 (t0) cc_final: 0.6810 (t0) REVERT: C 173 MET cc_start: 0.2387 (mmp) cc_final: 0.1106 (mtm) REVERT: C 432 TRP cc_start: 0.2917 (p90) cc_final: 0.2065 (p90) REVERT: D 4 LEU cc_start: -0.2717 (OUTLIER) cc_final: -0.4066 (mt) REVERT: D 36 TRP cc_start: 0.4756 (m100) cc_final: 0.4008 (m100) REVERT: F 5 GLN cc_start: 0.8547 (mm110) cc_final: 0.8147 (mp10) REVERT: F 50 PHE cc_start: 0.8190 (m-80) cc_final: 0.7919 (m-80) outliers start: 75 outliers final: 41 residues processed: 205 average time/residue: 0.3845 time to fit residues: 133.2013 Evaluate side-chains 182 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 139 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 314 optimal weight: 50.0000 chunk 292 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN B 953 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078266 restraints weight = 59445.663| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.01 r_work: 0.2864 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28443 Z= 0.125 Angle : 0.565 16.753 38787 Z= 0.281 Chirality : 0.045 0.438 4477 Planarity : 0.004 0.049 4933 Dihedral : 6.449 98.407 4569 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 2.51 % Allowed : 18.21 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3424 helix: 2.47 (0.20), residues: 648 sheet: 0.55 (0.16), residues: 935 loop : -0.62 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 101 HIS 0.005 0.001 HIS F 79 PHE 0.017 0.001 PHE B 370 TYR 0.019 0.001 TYR A1063 ARG 0.006 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 25) link_NAG-ASN : angle 3.84793 ( 75) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.00616 ( 45) hydrogen bonds : bond 0.04999 ( 1117) hydrogen bonds : angle 5.21604 ( 3084) SS BOND : bond 0.00254 ( 45) SS BOND : angle 0.91500 ( 90) covalent geometry : bond 0.00283 (28358) covalent geometry : angle 0.53764 (38577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 144 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7840 (tp40) REVERT: B 388 PHE cc_start: 0.8538 (m-80) cc_final: 0.8287 (m-80) REVERT: B 786 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8717 (ptpp) REVERT: C 173 MET cc_start: 0.2027 (mmp) cc_final: 0.1270 (mtm) REVERT: C 432 TRP cc_start: 0.2954 (p90) cc_final: 0.2159 (p90) REVERT: D 4 LEU cc_start: -0.2636 (OUTLIER) cc_final: -0.4107 (mt) REVERT: D 34 MET cc_start: 0.1518 (tpp) cc_final: 0.0746 (tmm) REVERT: D 36 TRP cc_start: 0.4592 (m100) cc_final: 0.4233 (m100) REVERT: F 5 GLN cc_start: 0.8582 (mm110) cc_final: 0.8225 (mp10) REVERT: F 50 PHE cc_start: 0.8266 (m-80) cc_final: 0.7566 (m-80) REVERT: F 104 TYR cc_start: 0.8247 (m-10) cc_final: 0.7947 (m-10) outliers start: 76 outliers final: 41 residues processed: 208 average time/residue: 0.3483 time to fit residues: 121.5723 Evaluate side-chains 179 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 340 optimal weight: 50.0000 chunk 269 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.143415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079805 restraints weight = 58830.477| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.34 r_work: 0.2851 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28443 Z= 0.130 Angle : 0.553 16.441 38787 Z= 0.274 Chirality : 0.045 0.383 4477 Planarity : 0.003 0.047 4933 Dihedral : 6.205 92.358 4569 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3424 helix: 2.50 (0.20), residues: 654 sheet: 0.57 (0.16), residues: 950 loop : -0.59 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 101 HIS 0.005 0.001 HIS F 79 PHE 0.014 0.001 PHE B 452 TYR 0.019 0.001 TYR A1063 ARG 0.006 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 25) link_NAG-ASN : angle 3.64590 ( 75) link_BETA1-4 : bond 0.00249 ( 15) link_BETA1-4 : angle 1.04509 ( 45) hydrogen bonds : bond 0.04782 ( 1117) hydrogen bonds : angle 5.05993 ( 3084) SS BOND : bond 0.00209 ( 45) SS BOND : angle 0.89108 ( 90) covalent geometry : bond 0.00302 (28358) covalent geometry : angle 0.52778 (38577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 139 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7867 (tp40) REVERT: B 736 MET cc_start: 0.9207 (tpp) cc_final: 0.8993 (ttt) REVERT: B 786 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8779 (ptpp) REVERT: C 172 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7296 (tt) REVERT: C 173 MET cc_start: 0.2314 (mmp) cc_final: 0.1614 (mtm) REVERT: C 432 TRP cc_start: 0.3029 (p90) cc_final: 0.2221 (p90) REVERT: D 4 LEU cc_start: -0.3246 (OUTLIER) cc_final: -0.4478 (mt) REVERT: D 36 TRP cc_start: 0.4625 (m100) cc_final: 0.4253 (m100) REVERT: F 5 GLN cc_start: 0.8623 (mm110) cc_final: 0.8283 (mp10) REVERT: F 38 ARG cc_start: 0.9292 (mtm110) cc_final: 0.8377 (tpp80) REVERT: F 50 PHE cc_start: 0.8396 (m-80) cc_final: 0.7722 (m-80) REVERT: F 98 VAL cc_start: 0.8039 (p) cc_final: 0.7795 (p) REVERT: F 104 TYR cc_start: 0.8397 (m-10) cc_final: 0.8066 (m-10) outliers start: 76 outliers final: 53 residues processed: 200 average time/residue: 0.3850 time to fit residues: 132.8761 Evaluate side-chains 190 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 312 optimal weight: 40.0000 chunk 193 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 chunk 274 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.142616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077291 restraints weight = 59313.806| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.99 r_work: 0.2853 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 28443 Z= 0.155 Angle : 0.560 16.545 38787 Z= 0.279 Chirality : 0.045 0.374 4477 Planarity : 0.003 0.047 4933 Dihedral : 5.801 71.491 4569 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 2.80 % Allowed : 17.94 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3424 helix: 2.46 (0.20), residues: 655 sheet: 0.59 (0.16), residues: 938 loop : -0.60 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 101 HIS 0.005 0.001 HIS F 79 PHE 0.031 0.001 PHE B 371 TYR 0.019 0.001 TYR A1063 ARG 0.006 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 25) link_NAG-ASN : angle 3.60483 ( 75) link_BETA1-4 : bond 0.00225 ( 15) link_BETA1-4 : angle 1.04430 ( 45) hydrogen bonds : bond 0.05032 ( 1117) hydrogen bonds : angle 5.04151 ( 3084) SS BOND : bond 0.00242 ( 45) SS BOND : angle 0.91046 ( 90) covalent geometry : bond 0.00368 (28358) covalent geometry : angle 0.53549 (38577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 135 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: B 570 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7580 (t0) REVERT: B 786 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8776 (ptpp) REVERT: C 172 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7359 (tt) REVERT: C 173 MET cc_start: 0.2390 (mmp) cc_final: 0.1831 (mtm) REVERT: C 432 TRP cc_start: 0.2966 (p90) cc_final: 0.2115 (p90) REVERT: D 4 LEU cc_start: -0.3124 (OUTLIER) cc_final: -0.4372 (mt) REVERT: D 34 MET cc_start: 0.1661 (tpp) cc_final: 0.1369 (tmm) REVERT: F 5 GLN cc_start: 0.8612 (mm110) cc_final: 0.8243 (mp10) REVERT: F 38 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8443 (tpp80) REVERT: F 50 PHE cc_start: 0.8355 (m-80) cc_final: 0.7649 (m-80) REVERT: F 67 PHE cc_start: 0.7446 (m-80) cc_final: 0.7201 (m-80) REVERT: F 104 TYR cc_start: 0.8193 (m-10) cc_final: 0.7927 (m-10) outliers start: 85 outliers final: 55 residues processed: 208 average time/residue: 0.3436 time to fit residues: 122.2244 Evaluate side-chains 193 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 79 optimal weight: 0.1980 chunk 141 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.142427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.077084 restraints weight = 59058.022| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.99 r_work: 0.2846 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 28443 Z= 0.162 Angle : 0.559 16.564 38787 Z= 0.278 Chirality : 0.045 0.360 4477 Planarity : 0.003 0.046 4933 Dihedral : 5.521 59.402 4567 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3424 helix: 2.47 (0.20), residues: 655 sheet: 0.63 (0.16), residues: 927 loop : -0.59 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 36 HIS 0.005 0.001 HIS F 79 PHE 0.016 0.001 PHE B 371 TYR 0.019 0.001 TYR A1063 ARG 0.004 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 25) link_NAG-ASN : angle 3.65696 ( 75) link_BETA1-4 : bond 0.00242 ( 15) link_BETA1-4 : angle 1.03214 ( 45) hydrogen bonds : bond 0.05039 ( 1117) hydrogen bonds : angle 5.03020 ( 3084) SS BOND : bond 0.00219 ( 45) SS BOND : angle 0.92936 ( 90) covalent geometry : bond 0.00386 (28358) covalent geometry : angle 0.53418 (38577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 131 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7847 (tp40) REVERT: B 570 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 786 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8764 (ptpp) REVERT: C 172 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7455 (tt) REVERT: C 173 MET cc_start: 0.2576 (mmp) cc_final: 0.2245 (mtm) REVERT: C 432 TRP cc_start: 0.2946 (p90) cc_final: 0.2105 (p90) REVERT: D 4 LEU cc_start: -0.2808 (OUTLIER) cc_final: -0.4363 (mt) REVERT: F 5 GLN cc_start: 0.8579 (mm110) cc_final: 0.8204 (mp10) REVERT: F 38 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8420 (tpp80) REVERT: F 50 PHE cc_start: 0.8320 (m-80) cc_final: 0.7633 (m-80) REVERT: F 67 PHE cc_start: 0.7502 (m-80) cc_final: 0.7274 (m-80) REVERT: F 104 TYR cc_start: 0.8108 (m-10) cc_final: 0.7855 (m-10) outliers start: 77 outliers final: 62 residues processed: 194 average time/residue: 0.3684 time to fit residues: 121.8319 Evaluate side-chains 196 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 233 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 342 optimal weight: 0.0570 chunk 269 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.141154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075563 restraints weight = 59079.206| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.00 r_work: 0.2812 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28443 Z= 0.208 Angle : 0.594 17.029 38787 Z= 0.298 Chirality : 0.046 0.372 4477 Planarity : 0.004 0.046 4933 Dihedral : 5.550 59.599 4567 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 2.64 % Allowed : 19.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3424 helix: 2.28 (0.20), residues: 661 sheet: 0.58 (0.16), residues: 931 loop : -0.66 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 36 HIS 0.004 0.001 HIS F 79 PHE 0.017 0.001 PHE B 371 TYR 0.020 0.001 TYR C1063 ARG 0.004 0.000 ARG A 991 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 25) link_NAG-ASN : angle 3.79938 ( 75) link_BETA1-4 : bond 0.00188 ( 15) link_BETA1-4 : angle 1.07974 ( 45) hydrogen bonds : bond 0.05659 ( 1117) hydrogen bonds : angle 5.13084 ( 3084) SS BOND : bond 0.00210 ( 45) SS BOND : angle 1.04335 ( 90) covalent geometry : bond 0.00497 (28358) covalent geometry : angle 0.56832 (38577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 132 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 310 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: B 570 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 736 MET cc_start: 0.9280 (tpp) cc_final: 0.8839 (ttt) REVERT: B 786 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: C 172 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7519 (tt) REVERT: C 432 TRP cc_start: 0.2901 (p90) cc_final: 0.2067 (p90) REVERT: D 4 LEU cc_start: -0.2859 (OUTLIER) cc_final: -0.4166 (mt) REVERT: F 5 GLN cc_start: 0.8598 (mm110) cc_final: 0.8217 (mp10) REVERT: F 50 PHE cc_start: 0.8314 (m-80) cc_final: 0.7571 (m-80) outliers start: 80 outliers final: 63 residues processed: 197 average time/residue: 0.3540 time to fit residues: 119.7430 Evaluate side-chains 195 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 14 optimal weight: 10.0000 chunk 320 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 51 optimal weight: 0.0670 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN ** F 76 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.141062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075594 restraints weight = 59092.729| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.99 r_work: 0.2827 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 28443 Z= 0.203 Angle : 0.584 17.014 38787 Z= 0.293 Chirality : 0.045 0.366 4477 Planarity : 0.004 0.047 4933 Dihedral : 5.514 59.847 4567 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.57 % Allowed : 19.13 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3424 helix: 2.25 (0.20), residues: 661 sheet: 0.53 (0.16), residues: 924 loop : -0.64 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP D 36 HIS 0.005 0.001 HIS F 79 PHE 0.021 0.001 PHE C 234 TYR 0.019 0.001 TYR C1063 ARG 0.006 0.000 ARG B 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 25) link_NAG-ASN : angle 3.70393 ( 75) link_BETA1-4 : bond 0.00220 ( 15) link_BETA1-4 : angle 1.01921 ( 45) hydrogen bonds : bond 0.05468 ( 1117) hydrogen bonds : angle 5.09868 ( 3084) SS BOND : bond 0.00222 ( 45) SS BOND : angle 0.99086 ( 90) covalent geometry : bond 0.00489 (28358) covalent geometry : angle 0.55920 (38577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 134 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8054 (tp40) REVERT: B 570 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7872 (t0) REVERT: B 736 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8976 (ttt) REVERT: B 786 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8894 (ptpp) REVERT: C 432 TRP cc_start: 0.3110 (p90) cc_final: 0.2242 (p90) REVERT: D 4 LEU cc_start: -0.3840 (OUTLIER) cc_final: -0.5252 (mt) REVERT: F 5 GLN cc_start: 0.8607 (mm110) cc_final: 0.8226 (mp10) REVERT: F 50 PHE cc_start: 0.8588 (m-80) cc_final: 0.7798 (m-80) outliers start: 78 outliers final: 63 residues processed: 195 average time/residue: 0.3525 time to fit residues: 117.5695 Evaluate side-chains 197 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 133 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN B 953 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.143146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078617 restraints weight = 58818.234| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.00 r_work: 0.2880 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28443 Z= 0.103 Angle : 0.541 16.351 38787 Z= 0.269 Chirality : 0.044 0.338 4477 Planarity : 0.003 0.046 4933 Dihedral : 5.250 59.910 4567 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.95 % Allowed : 19.72 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3424 helix: 2.50 (0.20), residues: 662 sheet: 0.68 (0.16), residues: 933 loop : -0.53 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP D 36 HIS 0.006 0.001 HIS F 79 PHE 0.023 0.001 PHE C 234 TYR 0.030 0.001 TYR F 104 ARG 0.004 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 25) link_NAG-ASN : angle 3.37517 ( 75) link_BETA1-4 : bond 0.00412 ( 15) link_BETA1-4 : angle 0.93122 ( 45) hydrogen bonds : bond 0.04383 ( 1117) hydrogen bonds : angle 4.85375 ( 3084) SS BOND : bond 0.00216 ( 45) SS BOND : angle 0.82495 ( 90) covalent geometry : bond 0.00231 (28358) covalent geometry : angle 0.51870 (38577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7809 (tp40) REVERT: B 452 PHE cc_start: 0.8425 (m-10) cc_final: 0.8180 (m-10) REVERT: B 570 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 736 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8682 (tpp) REVERT: B 786 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8812 (ptpp) REVERT: C 432 TRP cc_start: 0.3035 (p90) cc_final: 0.2201 (p90) REVERT: D 4 LEU cc_start: -0.3310 (OUTLIER) cc_final: -0.4688 (mt) REVERT: F 5 GLN cc_start: 0.8523 (mm110) cc_final: 0.8142 (mp10) REVERT: F 50 PHE cc_start: 0.8528 (m-80) cc_final: 0.7764 (m-80) REVERT: F 100 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8367 (ttpt) outliers start: 59 outliers final: 48 residues processed: 186 average time/residue: 0.3811 time to fit residues: 119.9781 Evaluate side-chains 184 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 304 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 161 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 248 optimal weight: 40.0000 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 897 GLN B 953 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.141602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076545 restraints weight = 59246.926| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.99 r_work: 0.2839 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28443 Z= 0.172 Angle : 0.568 16.578 38787 Z= 0.283 Chirality : 0.045 0.361 4477 Planarity : 0.003 0.047 4933 Dihedral : 5.250 59.954 4567 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.08 % Allowed : 19.95 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3424 helix: 2.38 (0.20), residues: 674 sheet: 0.64 (0.16), residues: 926 loop : -0.57 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP D 36 HIS 0.004 0.001 HIS F 79 PHE 0.024 0.001 PHE C 234 TYR 0.021 0.001 TYR F 104 ARG 0.008 0.000 ARG B 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 25) link_NAG-ASN : angle 3.49181 ( 75) link_BETA1-4 : bond 0.00224 ( 15) link_BETA1-4 : angle 1.02425 ( 45) hydrogen bonds : bond 0.05093 ( 1117) hydrogen bonds : angle 4.95713 ( 3084) SS BOND : bond 0.00213 ( 45) SS BOND : angle 0.95943 ( 90) covalent geometry : bond 0.00413 (28358) covalent geometry : angle 0.54486 (38577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18671.95 seconds wall clock time: 323 minutes 11.59 seconds (19391.59 seconds total)