Starting phenix.real_space_refine on Sun Jul 5 21:16:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqx_34038/07_2026/7yqx_34038.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 125 5.16 5 C 19156 2.51 5 N 4963 2.21 5 O 5924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30168 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8552 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.01, per 1000 atoms: 0.23 Number of scatterers: 30168 At special positions: 0 Unit cell: (187.25, 154.08, 184.04, 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 125 16.00 O 5924 8.00 N 4963 7.00 C 19156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 74 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 657 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG A1315 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 74 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 616 " " NAG B1311 " - " ASN B 657 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 74 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 343 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6978 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 56 sheets defined 18.9% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 4.069A pdb=" N GLY A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.883A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.730A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.590A pdb=" N VAL A 622 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.733A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.094A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.640A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.569A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.858A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.810A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.345A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.214A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.741A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.553A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.618A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.516A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.872A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.144A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.579A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.543A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.530A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.537A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.786A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.584A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.585A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.600A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.004A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.575A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.575A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.739A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.916A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.668A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.681A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.656A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.684A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.641A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.039A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.764A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.998A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.773A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.557A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.298A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.764A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.704A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.546A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 6.960A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.742A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.624A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.882A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.067A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.367A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.684A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 541 removed outlier: 3.802A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 573 through 576 removed outlier: 3.585A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.037A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.588A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.594A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.353A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.549A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.588A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.484A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.293A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.655A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.979A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 727 removed outlier: 6.982A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 49 through 51 removed outlier: 4.121A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AF5, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.396A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.231A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.231A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.704A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.278A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5290 1.33 - 1.45: 8570 1.45 - 1.58: 16848 1.58 - 1.70: 0 1.70 - 1.83: 158 Bond restraints: 30866 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C PRO B 330 " pdb=" O PRO B 330 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.83e+00 bond pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.42e+00 ... (remaining 30861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 40637 1.68 - 3.36: 1185 3.36 - 5.04: 152 5.04 - 6.72: 33 6.72 - 8.41: 9 Bond angle restraints: 42016 Sorted by residual: angle pdb=" C ASN B 331 " pdb=" CA ASN B 331 " pdb=" CB ASN B 331 " ideal model delta sigma weight residual 110.67 104.21 6.46 1.52e+00 4.33e-01 1.81e+01 angle pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" O PRO B 330 " ideal model delta sigma weight residual 122.13 117.46 4.67 1.23e+00 6.61e-01 1.44e+01 angle pdb=" N VAL C 620 " pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.98 -4.28 1.22e+00 6.72e-01 1.23e+01 angle pdb=" N ILE B1115 " pdb=" CA ILE B1115 " pdb=" C ILE B1115 " ideal model delta sigma weight residual 106.21 109.96 -3.75 1.07e+00 8.73e-01 1.23e+01 ... (remaining 42011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16059 17.92 - 35.83: 1397 35.83 - 53.75: 238 53.75 - 71.66: 25 71.66 - 89.58: 45 Dihedral angle restraints: 17764 sinusoidal: 6875 harmonic: 10889 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.41 -87.41 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.67 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.57 53.43 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4892 0.147 - 0.295: 30 0.295 - 0.442: 8 0.442 - 0.590: 1 0.590 - 0.737: 1 Chirality restraints: 4932 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 ... (remaining 4929 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1315 " 0.064 2.00e-02 2.50e+03 5.28e-02 3.48e+01 pdb=" C7 NAG A1315 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A1315 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1315 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG A1315 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 80 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO F 81 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO C 986 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.032 5.00e-02 4.00e+02 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1138 2.70 - 3.25: 30473 3.25 - 3.80: 45612 3.80 - 4.35: 56542 4.35 - 4.90: 94425 Nonbonded interactions: 228190 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.151 3.040 nonbonded pdb=" O ALA I 24 " pdb=" OG1 THR I 77 " model vdw 2.175 3.040 nonbonded pdb=" O VAL F 3 " pdb=" OG SER F 26 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.195 3.040 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.203 3.120 ... (remaining 228185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 25 through 1314) selection = chain 'B' selection = (chain 'C' and (resid 25 through 377 or (resid 378 and (name N or name CA or nam \ e C or name O or name CB )) or resid 379 through 385 or (resid 386 and (name N o \ r name CA or name C or name O or name CB )) or resid 387 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'F' and resid 1 through 108) selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.200 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.055 30973 Z= 0.211 Angle : 0.720 17.263 42299 Z= 0.353 Chirality : 0.051 0.737 4932 Planarity : 0.004 0.079 5352 Dihedral : 14.127 89.577 10672 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.83 % Favored : 91.09 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.13), residues: 3727 helix: -0.16 (0.21), residues: 607 sheet: -0.62 (0.20), residues: 702 loop : -2.09 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.020 0.001 TYR C 160 PHE 0.026 0.001 PHE C 906 TRP 0.029 0.002 TRP H 117 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (30866) covalent geometry : angle 0.67046 / 0.34 (42016) SS BOND : bond 0.00238 / 0.15 ( 38) SS BOND : angle 1.32757 / 0.95 ( 76) hydrogen bonds : bond 0.22505 / 15.19 ( 808) hydrogen bonds : angle 8.84573 / 6.13 ( 2205) link_BETA1-4 : bond 0.00643 / 0.41 ( 13) link_BETA1-4 : angle 3.21191 / 2.20 ( 39) link_BETA1-6 : bond 0.00328 / 0.16 ( 2) link_BETA1-6 : angle 1.40071 / 0.80 ( 6) link_NAG-ASN : bond 0.00781 / 0.53 ( 54) link_NAG-ASN : angle 3.92353 / 2.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5369 (m-80) cc_final: 0.5111 (m-80) REVERT: A 508 TYR cc_start: 0.6544 (m-10) cc_final: 0.6124 (m-10) REVERT: A 740 MET cc_start: 0.8259 (tpp) cc_final: 0.8004 (tpt) REVERT: B 186 PHE cc_start: 0.7639 (m-80) cc_final: 0.7248 (m-80) REVERT: C 201 PHE cc_start: 0.7665 (t80) cc_final: 0.7456 (t80) REVERT: C 396 TYR cc_start: 0.7152 (m-80) cc_final: 0.6195 (m-80) REVERT: C 529 LYS cc_start: 0.8843 (pptt) cc_final: 0.8629 (ptpp) REVERT: C 985 ASP cc_start: 0.8371 (t0) cc_final: 0.7991 (p0) REVERT: H 117 TRP cc_start: 0.7114 (m100) cc_final: 0.6555 (m-10) REVERT: F 37 TYR cc_start: 0.8219 (m-10) cc_final: 0.7979 (m-80) REVERT: F 50 TYR cc_start: 0.6443 (p90) cc_final: 0.5871 (p90) outliers start: 2 outliers final: 1 residues processed: 212 average time/residue: 0.1562 time to fit residues: 56.2469 Evaluate side-chains 160 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 895 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 450 ASN C 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.151024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.122216 restraints weight = 99922.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116065 restraints weight = 97762.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.114963 restraints weight = 85788.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.114525 restraints weight = 70110.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114654 restraints weight = 66935.750| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30973 Z= 0.150 Angle : 0.685 15.665 42299 Z= 0.330 Chirality : 0.048 0.475 4932 Planarity : 0.004 0.058 5352 Dihedral : 4.618 29.386 4046 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.20 % Favored : 90.77 % Rotamer: Outliers : 0.56 % Allowed : 7.12 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3727 helix: 0.33 (0.21), residues: 634 sheet: -0.47 (0.20), residues: 693 loop : -2.17 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.020 0.001 TYR B1067 PHE 0.026 0.001 PHE A 220 TRP 0.025 0.001 TRP H 47 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (30866) covalent geometry : angle 0.63307 / 0.32 (42016) SS BOND : bond 0.00264 / 0.15 ( 38) SS BOND : angle 1.36303 / 0.98 ( 76) hydrogen bonds : bond 0.05253 / 3.57 ( 808) hydrogen bonds : angle 6.43683 / 4.52 ( 2205) link_BETA1-4 : bond 0.00750 / 0.46 ( 13) link_BETA1-4 : angle 2.87994 / 1.97 ( 39) link_BETA1-6 : bond 0.00317 / 0.16 ( 2) link_BETA1-6 : angle 1.23239 / 0.66 ( 6) link_NAG-ASN : bond 0.00760 / 0.51 ( 54) link_NAG-ASN : angle 3.94700 / 2.51 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5142 (m-80) cc_final: 0.4811 (m-80) REVERT: A 508 TYR cc_start: 0.6394 (m-10) cc_final: 0.6042 (m-10) REVERT: A 740 MET cc_start: 0.8422 (tpp) cc_final: 0.8198 (tpt) REVERT: C 201 PHE cc_start: 0.7781 (t80) cc_final: 0.7524 (t80) REVERT: C 396 TYR cc_start: 0.7065 (m-80) cc_final: 0.6288 (m-80) REVERT: C 592 PHE cc_start: 0.8368 (p90) cc_final: 0.8108 (p90) REVERT: H 47 TRP cc_start: 0.7857 (t60) cc_final: 0.7266 (p-90) REVERT: H 114 PHE cc_start: 0.8417 (m-80) cc_final: 0.8119 (m-80) REVERT: H 117 TRP cc_start: 0.6991 (m100) cc_final: 0.6666 (m-10) REVERT: F 43 GLN cc_start: 0.8674 (mt0) cc_final: 0.8455 (mt0) REVERT: F 50 TYR cc_start: 0.6100 (p90) cc_final: 0.5682 (p90) outliers start: 18 outliers final: 12 residues processed: 187 average time/residue: 0.1730 time to fit residues: 54.3987 Evaluate side-chains 163 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 229 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 358 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN B 519 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.132970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087295 restraints weight = 91769.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087132 restraints weight = 56899.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087674 restraints weight = 54551.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088525 restraints weight = 37727.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088636 restraints weight = 33252.829| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 30973 Z= 0.362 Angle : 0.848 14.679 42299 Z= 0.416 Chirality : 0.053 0.512 4932 Planarity : 0.005 0.065 5352 Dihedral : 5.219 29.089 4044 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.38 % Favored : 88.60 % Rotamer: Outliers : 1.80 % Allowed : 11.46 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.13), residues: 3727 helix: -0.26 (0.20), residues: 632 sheet: -0.83 (0.20), residues: 695 loop : -2.39 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 237 TYR 0.025 0.002 TYR C 160 PHE 0.042 0.002 PHE B1121 TRP 0.015 0.002 TRP H 50 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.36 (30866) covalent geometry : angle 0.80293 / 0.41 (42016) SS BOND : bond 0.00360 / 0.23 ( 38) SS BOND : angle 1.54367 / 1.10 ( 76) hydrogen bonds : bond 0.06099 / 4.12 ( 808) hydrogen bonds : angle 6.71932 / 4.70 ( 2205) link_BETA1-4 : bond 0.00953 / 0.61 ( 13) link_BETA1-4 : angle 3.03518 / 2.07 ( 39) link_BETA1-6 : bond 0.00148 / 0.07 ( 2) link_BETA1-6 : angle 1.56652 / 0.82 ( 6) link_NAG-ASN : bond 0.00810 / 0.52 ( 54) link_NAG-ASN : angle 4.14336 / 2.66 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7326 (mpp80) REVERT: A 396 TYR cc_start: 0.5679 (m-80) cc_final: 0.5414 (m-80) REVERT: A 740 MET cc_start: 0.8636 (tpp) cc_final: 0.8428 (tpt) REVERT: A 902 MET cc_start: 0.9397 (tpt) cc_final: 0.9072 (tpt) REVERT: B 127 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 186 PHE cc_start: 0.7751 (m-80) cc_final: 0.7339 (m-80) REVERT: B 368 LEU cc_start: 0.9397 (mm) cc_final: 0.9089 (pp) REVERT: B 660 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: H 10 GLU cc_start: 0.2448 (mp0) cc_final: 0.2121 (mp0) REVERT: H 47 TRP cc_start: 0.8357 (t60) cc_final: 0.7992 (p-90) outliers start: 58 outliers final: 36 residues processed: 206 average time/residue: 0.1685 time to fit residues: 59.0670 Evaluate side-chains 187 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 213 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 278 optimal weight: 0.3980 chunk 163 optimal weight: 4.9990 chunk 336 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS F 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.134477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088692 restraints weight = 90874.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089450 restraints weight = 55500.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090708 restraints weight = 39673.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091384 restraints weight = 30182.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.091113 restraints weight = 28747.551| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30973 Z= 0.215 Angle : 0.721 14.138 42299 Z= 0.349 Chirality : 0.049 0.479 4932 Planarity : 0.005 0.069 5352 Dihedral : 4.985 28.260 4044 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.53 % Favored : 90.45 % Rotamer: Outliers : 2.20 % Allowed : 14.74 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 3727 helix: 0.01 (0.21), residues: 636 sheet: -0.71 (0.20), residues: 691 loop : -2.37 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.021 0.001 TYR B1067 PHE 0.027 0.002 PHE B1121 TRP 0.009 0.002 TRP H 47 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (30866) covalent geometry : angle 0.67244 / 0.34 (42016) SS BOND : bond 0.00305 / 0.19 ( 38) SS BOND : angle 1.42271 / 1.02 ( 76) hydrogen bonds : bond 0.05041 / 3.44 ( 808) hydrogen bonds : angle 6.26072 / 4.38 ( 2205) link_BETA1-4 : bond 0.00767 / 0.49 ( 13) link_BETA1-4 : angle 2.83326 / 1.93 ( 39) link_BETA1-6 : bond 0.00260 / 0.13 ( 2) link_BETA1-6 : angle 1.41649 / 0.75 ( 6) link_NAG-ASN : bond 0.00716 / 0.47 ( 54) link_NAG-ASN : angle 3.93362 / 2.52 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: A 396 TYR cc_start: 0.5834 (m-80) cc_final: 0.5584 (m-80) REVERT: B 127 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 186 PHE cc_start: 0.7670 (m-80) cc_final: 0.7233 (m-80) REVERT: B 306 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9119 (m-80) REVERT: B 368 LEU cc_start: 0.9365 (mm) cc_final: 0.9086 (pp) REVERT: C 396 TYR cc_start: 0.7096 (m-80) cc_final: 0.6076 (m-10) REVERT: H 47 TRP cc_start: 0.8357 (t60) cc_final: 0.7862 (p-90) REVERT: H 95 TYR cc_start: 0.7604 (m-80) cc_final: 0.7246 (m-10) REVERT: F 50 TYR cc_start: 0.6491 (p90) cc_final: 0.5773 (p90) REVERT: F 78 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7461 (tpm170) outliers start: 71 outliers final: 48 residues processed: 213 average time/residue: 0.1680 time to fit residues: 61.5261 Evaluate side-chains 201 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 164 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.138758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098007 restraints weight = 95003.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096095 restraints weight = 66093.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096275 restraints weight = 59960.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096596 restraints weight = 56554.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096717 restraints weight = 50888.516| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30973 Z= 0.145 Angle : 0.674 13.621 42299 Z= 0.323 Chirality : 0.048 0.463 4932 Planarity : 0.004 0.069 5352 Dihedral : 4.782 32.989 4044 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.34 % Favored : 90.64 % Rotamer: Outliers : 2.14 % Allowed : 16.10 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3727 helix: 0.30 (0.21), residues: 630 sheet: -0.69 (0.19), residues: 732 loop : -2.32 (0.12), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.019 0.001 TYR C 160 PHE 0.027 0.001 PHE H 29 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (30866) covalent geometry : angle 0.62204 / 0.31 (42016) SS BOND : bond 0.00262 / 0.16 ( 38) SS BOND : angle 1.84640 / 1.35 ( 76) hydrogen bonds : bond 0.04484 / 3.05 ( 808) hydrogen bonds : angle 5.91776 / 4.15 ( 2205) link_BETA1-4 : bond 0.00701 / 0.43 ( 13) link_BETA1-4 : angle 2.62019 / 1.78 ( 39) link_BETA1-6 : bond 0.00363 / 0.19 ( 2) link_BETA1-6 : angle 1.29769 / 0.70 ( 6) link_NAG-ASN : bond 0.00712 / 0.48 ( 54) link_NAG-ASN : angle 3.87003 / 2.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5798 (m-80) cc_final: 0.5525 (m-80) REVERT: B 127 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8049 (p) REVERT: B 186 PHE cc_start: 0.7684 (m-80) cc_final: 0.7246 (m-80) REVERT: B 189 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 306 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9190 (m-80) REVERT: B 368 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9148 (pp) REVERT: C 170 TYR cc_start: 0.6518 (t80) cc_final: 0.6258 (t80) REVERT: H 47 TRP cc_start: 0.8433 (t60) cc_final: 0.7827 (p-90) REVERT: H 70 MET cc_start: 0.4914 (ptt) cc_final: 0.4510 (ptt) REVERT: H 95 TYR cc_start: 0.7581 (m-80) cc_final: 0.7216 (m-10) REVERT: F 50 TYR cc_start: 0.6493 (p90) cc_final: 0.5824 (p90) REVERT: F 78 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7331 (tpt90) outliers start: 69 outliers final: 49 residues processed: 208 average time/residue: 0.1629 time to fit residues: 58.3569 Evaluate side-chains 201 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 230 optimal weight: 10.0000 chunk 356 optimal weight: 0.5980 chunk 365 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 233 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.150433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.121957 restraints weight = 99702.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.115234 restraints weight = 101283.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.114358 restraints weight = 88586.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.114349 restraints weight = 65989.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.114338 restraints weight = 61299.579| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30973 Z= 0.121 Angle : 0.641 13.076 42299 Z= 0.308 Chirality : 0.047 0.458 4932 Planarity : 0.004 0.066 5352 Dihedral : 4.541 27.080 4044 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.40 % Favored : 91.57 % Rotamer: Outliers : 2.29 % Allowed : 16.50 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 3727 helix: 0.60 (0.21), residues: 625 sheet: -0.56 (0.19), residues: 731 loop : -2.23 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.020 0.001 TYR C 160 PHE 0.020 0.001 PHE A 192 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (30866) covalent geometry : angle 0.59433 / 0.30 (42016) SS BOND : bond 0.00243 / 0.14 ( 38) SS BOND : angle 1.31039 / 0.95 ( 76) hydrogen bonds : bond 0.03979 / 2.70 ( 808) hydrogen bonds : angle 5.61031 / 3.94 ( 2205) link_BETA1-4 : bond 0.00660 / 0.41 ( 13) link_BETA1-4 : angle 2.33694 / 1.58 ( 39) link_BETA1-6 : bond 0.00384 / 0.20 ( 2) link_BETA1-6 : angle 1.21450 / 0.66 ( 6) link_NAG-ASN : bond 0.00703 / 0.47 ( 54) link_NAG-ASN : angle 3.68878 / 2.39 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7110 (m-80) cc_final: 0.6827 (m-80) REVERT: A 396 TYR cc_start: 0.5497 (m-80) cc_final: 0.4880 (m-80) REVERT: A 569 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8828 (tt) REVERT: B 186 PHE cc_start: 0.7310 (m-80) cc_final: 0.7013 (m-80) REVERT: B 189 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 660 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.6432 (m-10) REVERT: C 396 TYR cc_start: 0.6905 (m-80) cc_final: 0.6172 (m-80) REVERT: H 47 TRP cc_start: 0.7724 (t60) cc_final: 0.7418 (p-90) REVERT: F 50 TYR cc_start: 0.5898 (p90) cc_final: 0.5332 (p90) outliers start: 74 outliers final: 49 residues processed: 217 average time/residue: 0.1655 time to fit residues: 62.0159 Evaluate side-chains 201 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 131 optimal weight: 7.9990 chunk 241 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 341 optimal weight: 2.9990 chunk 261 optimal weight: 0.0270 chunk 259 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 121 ASN C 360 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.148379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.116140 restraints weight = 99131.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.115663 restraints weight = 90627.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116053 restraints weight = 70127.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115611 restraints weight = 57235.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115720 restraints weight = 55447.401| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30973 Z= 0.225 Angle : 0.718 12.485 42299 Z= 0.347 Chirality : 0.049 0.478 4932 Planarity : 0.005 0.071 5352 Dihedral : 4.819 26.597 4044 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.46 % Favored : 89.51 % Rotamer: Outliers : 2.91 % Allowed : 16.35 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 3727 helix: 0.34 (0.21), residues: 625 sheet: -0.74 (0.19), residues: 751 loop : -2.29 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.023 0.002 TYR C 160 PHE 0.030 0.002 PHE B1121 TRP 0.018 0.002 TRP H 36 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (30866) covalent geometry : angle 0.67309 / 0.34 (42016) SS BOND : bond 0.00325 / 0.22 ( 38) SS BOND : angle 1.61355 / 1.11 ( 76) hydrogen bonds : bond 0.04724 / 3.19 ( 808) hydrogen bonds : angle 5.87684 / 4.12 ( 2205) link_BETA1-4 : bond 0.00719 / 0.45 ( 13) link_BETA1-4 : angle 2.47206 / 1.68 ( 39) link_BETA1-6 : bond 0.00265 / 0.14 ( 2) link_BETA1-6 : angle 1.41209 / 0.75 ( 6) link_NAG-ASN : bond 0.00662 / 0.43 ( 54) link_NAG-ASN : angle 3.76319 / 2.44 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 154 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5212 (m-80) cc_final: 0.4693 (m-80) REVERT: A 902 MET cc_start: 0.9306 (tpt) cc_final: 0.9030 (tpt) REVERT: B 660 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.6455 (m-10) REVERT: B 1050 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7964 (ptp) REVERT: C 396 TYR cc_start: 0.6757 (m-80) cc_final: 0.6170 (m-10) REVERT: F 50 TYR cc_start: 0.5527 (p90) cc_final: 0.5026 (p90) outliers start: 94 outliers final: 72 residues processed: 223 average time/residue: 0.1617 time to fit residues: 62.0118 Evaluate side-chains 216 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 339 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 359 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 196 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.148847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.117874 restraints weight = 99696.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.118037 restraints weight = 91949.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.117626 restraints weight = 66193.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.116309 restraints weight = 65624.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.116716 restraints weight = 61273.636| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30973 Z= 0.178 Angle : 0.704 19.160 42299 Z= 0.337 Chirality : 0.048 0.463 4932 Planarity : 0.004 0.073 5352 Dihedral : 4.813 28.779 4044 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.50 % Favored : 90.47 % Rotamer: Outliers : 2.79 % Allowed : 16.90 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3727 helix: 0.36 (0.21), residues: 634 sheet: -0.67 (0.19), residues: 757 loop : -2.32 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.021 0.001 TYR C 160 PHE 0.033 0.001 PHE F 98 TRP 0.044 0.002 TRP H 47 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (30866) covalent geometry : angle 0.65296 / 0.33 (42016) SS BOND : bond 0.00278 / 0.17 ( 38) SS BOND : angle 1.47230 / 1.04 ( 76) hydrogen bonds : bond 0.04423 / 2.99 ( 808) hydrogen bonds : angle 5.73848 / 4.03 ( 2205) link_BETA1-4 : bond 0.00688 / 0.43 ( 13) link_BETA1-4 : angle 2.46379 / 1.67 ( 39) link_BETA1-6 : bond 0.00313 / 0.16 ( 2) link_BETA1-6 : angle 1.33045 / 0.71 ( 6) link_NAG-ASN : bond 0.00710 / 0.49 ( 54) link_NAG-ASN : angle 4.01768 / 2.61 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 148 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5335 (m-80) cc_final: 0.4814 (m-80) REVERT: A 902 MET cc_start: 0.9310 (tpt) cc_final: 0.9043 (tpt) REVERT: B 660 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: B 1050 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7713 (ptp) REVERT: C 1092 GLU cc_start: 0.7605 (pm20) cc_final: 0.7039 (pm20) REVERT: H 47 TRP cc_start: 0.7126 (t60) cc_final: 0.6880 (p-90) REVERT: F 50 TYR cc_start: 0.5560 (p90) cc_final: 0.5029 (p90) REVERT: F 78 ARG cc_start: 0.7169 (tpp-160) cc_final: 0.6964 (tpt90) outliers start: 90 outliers final: 78 residues processed: 214 average time/residue: 0.1590 time to fit residues: 58.2191 Evaluate side-chains 223 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 143 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 0.0020 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.149240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.120714 restraints weight = 99701.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.114643 restraints weight = 101655.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.113131 restraints weight = 92041.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.113034 restraints weight = 72453.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.113298 restraints weight = 62249.440| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30973 Z= 0.154 Angle : 0.677 12.378 42299 Z= 0.326 Chirality : 0.047 0.451 4932 Planarity : 0.004 0.078 5352 Dihedral : 4.744 29.982 4044 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.50 % Favored : 90.47 % Rotamer: Outliers : 2.63 % Allowed : 17.24 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3727 helix: 0.49 (0.21), residues: 634 sheet: -0.61 (0.19), residues: 749 loop : -2.28 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.020 0.001 TYR C 160 PHE 0.025 0.001 PHE F 98 TRP 0.042 0.002 TRP H 47 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (30866) covalent geometry : angle 0.63364 / 0.32 (42016) SS BOND : bond 0.00257 / 0.16 ( 38) SS BOND : angle 1.27387 / 0.92 ( 76) hydrogen bonds : bond 0.04196 / 2.84 ( 808) hydrogen bonds : angle 5.61370 / 3.94 ( 2205) link_BETA1-4 : bond 0.00662 / 0.41 ( 13) link_BETA1-4 : angle 2.38748 / 1.62 ( 39) link_BETA1-6 : bond 0.00321 / 0.17 ( 2) link_BETA1-6 : angle 1.26372 / 0.69 ( 6) link_NAG-ASN : bond 0.00671 / 0.46 ( 54) link_NAG-ASN : angle 3.67589 / 2.38 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 153 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5556 (m-80) cc_final: 0.5000 (m-80) REVERT: A 633 TRP cc_start: 0.4044 (OUTLIER) cc_final: 0.3648 (p-90) REVERT: B 73 THR cc_start: 0.4880 (OUTLIER) cc_final: 0.4280 (p) REVERT: B 660 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 1050 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7866 (ptp) REVERT: C 396 TYR cc_start: 0.7180 (m-80) cc_final: 0.6255 (m-80) REVERT: C 1092 GLU cc_start: 0.7553 (pm20) cc_final: 0.6986 (pm20) REVERT: H 47 TRP cc_start: 0.7660 (t60) cc_final: 0.7392 (p-90) REVERT: F 50 TYR cc_start: 0.5781 (p90) cc_final: 0.5126 (p90) REVERT: F 78 ARG cc_start: 0.7500 (tpp-160) cc_final: 0.7153 (tpt90) outliers start: 85 outliers final: 74 residues processed: 217 average time/residue: 0.1731 time to fit residues: 64.9284 Evaluate side-chains 225 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 147 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 178 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 chunk 324 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.150649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.119918 restraints weight = 99145.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.118488 restraints weight = 88246.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.114820 restraints weight = 58488.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114457 restraints weight = 60173.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.114684 restraints weight = 60532.933| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30973 Z= 0.116 Angle : 0.672 20.148 42299 Z= 0.321 Chirality : 0.047 0.465 4932 Planarity : 0.004 0.075 5352 Dihedral : 4.599 27.609 4044 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 2.26 % Allowed : 17.93 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.13), residues: 3727 helix: 0.76 (0.22), residues: 627 sheet: -0.51 (0.19), residues: 742 loop : -2.22 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.027 0.001 TYR C 453 PHE 0.021 0.001 PHE F 98 TRP 0.052 0.002 TRP F 36 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (30866) covalent geometry : angle 0.62049 / 0.31 (42016) SS BOND : bond 0.00233 / 0.13 ( 38) SS BOND : angle 1.14555 / 0.81 ( 76) hydrogen bonds : bond 0.03829 / 2.59 ( 808) hydrogen bonds : angle 5.40551 / 3.80 ( 2205) link_BETA1-4 : bond 0.00644 / 0.39 ( 13) link_BETA1-4 : angle 2.25243 / 1.52 ( 39) link_BETA1-6 : bond 0.00427 / 0.22 ( 2) link_BETA1-6 : angle 1.23194 / 0.67 ( 6) link_NAG-ASN : bond 0.00696 / 0.47 ( 54) link_NAG-ASN : angle 4.03697 / 2.71 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 152 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5534 (m-80) cc_final: 0.4998 (m-80) REVERT: A 633 TRP cc_start: 0.4007 (OUTLIER) cc_final: 0.3380 (p-90) REVERT: A 957 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 660 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: B 1050 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7741 (ptp) REVERT: C 396 TYR cc_start: 0.7073 (m-80) cc_final: 0.6147 (m-10) REVERT: C 1092 GLU cc_start: 0.7516 (pm20) cc_final: 0.6998 (pm20) REVERT: F 50 TYR cc_start: 0.5769 (p90) cc_final: 0.5197 (p90) REVERT: F 78 ARG cc_start: 0.7584 (tpp-160) cc_final: 0.7180 (tpt90) outliers start: 73 outliers final: 62 residues processed: 206 average time/residue: 0.1764 time to fit residues: 62.1269 Evaluate side-chains 213 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 355 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.116930 restraints weight = 99581.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.113897 restraints weight = 95246.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.109675 restraints weight = 77876.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.109761 restraints weight = 74884.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.110256 restraints weight = 66152.353| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30973 Z= 0.241 Angle : 0.748 15.292 42299 Z= 0.362 Chirality : 0.049 0.489 4932 Planarity : 0.005 0.073 5352 Dihedral : 4.931 26.392 4044 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.03 % Favored : 88.95 % Rotamer: Outliers : 2.29 % Allowed : 18.14 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3727 helix: 0.37 (0.21), residues: 631 sheet: -0.59 (0.19), residues: 750 loop : -2.33 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.023 0.002 TYR C 160 PHE 0.032 0.002 PHE B1121 TRP 0.063 0.003 TRP H 47 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (30866) covalent geometry : angle 0.70092 / 0.35 (42016) SS BOND : bond 0.00317 / 0.21 ( 38) SS BOND : angle 1.41755 / 1.03 ( 76) hydrogen bonds : bond 0.04731 / 3.18 ( 808) hydrogen bonds : angle 5.79796 / 4.06 ( 2205) link_BETA1-4 : bond 0.00757 / 0.48 ( 13) link_BETA1-4 : angle 2.51513 / 1.71 ( 39) link_BETA1-6 : bond 0.00218 / 0.11 ( 2) link_BETA1-6 : angle 1.39482 / 0.75 ( 6) link_NAG-ASN : bond 0.00698 / 0.49 ( 54) link_NAG-ASN : angle 4.03446 / 2.67 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.13 seconds wall clock time: 84 minutes 31.24 seconds (5071.24 seconds total)