Starting phenix.real_space_refine on Sun Jul 5 16:39:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnc_32038/07_2026/7vnc_32038.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3214 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16987 2.51 5 N 4397 2.21 5 O 5212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 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: 26716 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "V" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "B" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8364 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.60, per 1000 atoms: 0.25 Number of scatterers: 26716 At special positions: 0 Unit cell: (171.366, 174.408, 149.058, 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 120 16.00 O 5212 8.00 N 4397 7.00 C 16987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 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 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.02 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 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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 15 " - pdb=" SG CYS B 136 " distance=2.04 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 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " 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 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 D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " NAG N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 17 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 343 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG D 1 " - " ASN C 165 " " NAG E 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1134 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C 801 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6212 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 49 sheets defined 23.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.538A pdb=" N VAL C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.539A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.714A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.792A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.979A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.519A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.545A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.911A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 4.213A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.509A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 891 removed outlier: 4.235A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 4.507A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.625A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.945A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.314A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.133A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 30 removed outlier: 3.637A pdb=" N PHE V 29 " --> pdb=" O ASP V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 Processing helix chain 'V' and resid 99 through 102 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.511A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.925A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.880A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.338A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.650A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.309A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.970A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.921A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.507A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.548A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.500A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.598A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.773A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.578A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.894A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1146' Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.702A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.934A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.368A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.824A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.485A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.512A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.041A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.825A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.852A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.634A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.796A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.493A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.540A 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 removed outlier: 4.006A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.809A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.556A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.076A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.162A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.739A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.787A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.114A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 323 through 328 removed outlier: 4.427A pdb=" N ASN C 540 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL C 327 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 323 through 328 removed outlier: 4.427A pdb=" N ASN C 540 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL C 327 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.598A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.662A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 712 through 717 removed outlier: 6.595A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 720 through 728 removed outlier: 3.730A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.466A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.576A pdb=" N HIS C1083 " --> pdb=" O LYS C1086 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 46 through 47 removed outlier: 4.037A pdb=" N GLU V 46 " --> pdb=" O ARG V 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 46 through 47 removed outlier: 4.037A pdb=" N GLU V 46 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR V 94 " --> pdb=" O VAL V 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 68 through 71 removed outlier: 3.837A pdb=" N THR V 68 " --> pdb=" O GLN V 81 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN V 81 " --> pdb=" O THR V 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.814A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.834A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.052A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC8, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.540A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 551 through 554 Processing sheet with id=AD2, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.134A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.449A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'A' and resid 712 through 728 removed outlier: 3.669A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1050 through 1051 removed outlier: 4.204A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.401A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.617A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 225 through 229 removed outlier: 4.291A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.925A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AE4, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.950A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.704A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 712 through 717 removed outlier: 6.694A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B1104 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 720 through 727 removed outlier: 3.744A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 720 through 727 Processing sheet with id=AF3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'B' and resid 1089 through 1090 729 hydrogen bonds defined for protein. 1935 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: 6.90 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4331 1.31 - 1.44: 7515 1.44 - 1.57: 15319 1.57 - 1.70: 2 1.70 - 1.83: 154 Bond restraints: 27321 Sorted by residual: bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.477 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C7 NAG M 2 " pdb=" N2 NAG M 2 " ideal model delta sigma weight residual 1.346 1.476 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C7 NAG A1304 " pdb=" N2 NAG A1304 " ideal model delta sigma weight residual 1.346 1.476 -0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 27316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 36333 2.52 - 5.03: 740 5.03 - 7.55: 89 7.55 - 10.06: 14 10.06 - 12.58: 1 Bond angle restraints: 37177 Sorted by residual: angle pdb=" CA PRO B 225 " pdb=" N PRO B 225 " pdb=" CD PRO B 225 " ideal model delta sigma weight residual 112.00 99.42 12.58 1.40e+00 5.10e-01 8.07e+01 angle pdb=" N PRO B 225 " pdb=" CD PRO B 225 " pdb=" CG PRO B 225 " ideal model delta sigma weight residual 103.20 93.63 9.57 1.50e+00 4.44e-01 4.07e+01 angle pdb=" N PHE B 186 " pdb=" CA PHE B 186 " pdb=" C PHE B 186 " ideal model delta sigma weight residual 113.18 107.08 6.10 1.33e+00 5.65e-01 2.10e+01 angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 112.96 108.90 4.06 1.00e+00 1.00e+00 1.65e+01 angle pdb=" C THR B 20 " pdb=" N ARG B 21 " pdb=" CA ARG B 21 " ideal model delta sigma weight residual 122.46 115.51 6.95 1.80e+00 3.09e-01 1.49e+01 ... (remaining 37172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14221 17.98 - 35.95: 1290 35.95 - 53.93: 241 53.93 - 71.90: 29 71.90 - 89.88: 26 Dihedral angle restraints: 15807 sinusoidal: 6138 harmonic: 9669 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -162.35 76.35 1 1.00e+01 1.00e-02 7.33e+01 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 -11.27 -74.73 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -30.17 -55.83 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 15804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3831 0.076 - 0.152: 460 0.152 - 0.228: 45 0.228 - 0.304: 4 0.304 - 0.380: 3 Chirality restraints: 4343 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 4340 not shown) Planarity restraints: 4787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " 0.106 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO B 225 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 811 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO C 812 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 812 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 812 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 987 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.033 5.00e-02 4.00e+02 ... (remaining 4784 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 739 2.70 - 3.25: 25785 3.25 - 3.80: 39381 3.80 - 4.35: 51911 4.35 - 4.90: 85510 Nonbonded interactions: 203326 Sorted by model distance: nonbonded pdb=" OH TYR B 351 " pdb=" ND2 ASN B 422 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.188 3.040 nonbonded pdb=" O SER C 71 " pdb=" OG1 THR C 76 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASN C 978 " pdb=" OG1 THR B 547 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG B 905 " pdb=" O LEU B1049 " model vdw 2.210 3.120 ... (remaining 203321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 334 or resid 336 through 1303)) selection = (chain 'B' and resid 14 through 1303) selection = (chain 'C' and (resid 14 through 334 or resid 336 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.450 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.172 27399 Z= 0.445 Angle : 0.790 15.557 37384 Z= 0.354 Chirality : 0.049 0.380 4343 Planarity : 0.004 0.150 4754 Dihedral : 14.157 89.877 9514 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.21 (0.14), residues: 3291 helix: -1.28 (0.20), residues: 589 sheet: -0.53 (0.22), residues: 589 loop : -1.89 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 454 TYR 0.023 0.001 TYR B 351 PHE 0.023 0.001 PHE C 377 TRP 0.031 0.002 TRP C 353 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.45 (27321) covalent geometry : angle 0.76633 / 0.35 (37177) SS BOND : bond 0.00288 / 0.22 ( 27) SS BOND : angle 1.37945 / 0.97 ( 54) hydrogen bonds : bond 0.29487 / 19.66 ( 719) hydrogen bonds : angle 10.32058 / 7.19 ( 1935) link_BETA1-4 : bond 0.00536 / 0.38 ( 18) link_BETA1-4 : angle 1.53951 / 0.99 ( 54) link_NAG-ASN : bond 0.00647 / 0.46 ( 33) link_NAG-ASN : angle 3.60228 / 2.20 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9049 (tpp) cc_final: 0.8687 (ttt) REVERT: B 358 ILE cc_start: 0.8387 (mt) cc_final: 0.8164 (tt) REVERT: B 454 ARG cc_start: 0.6296 (ttt-90) cc_final: 0.6034 (ptm160) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1746 time to fit residues: 93.3673 Evaluate side-chains 231 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 ASN C 448 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN A 121 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 901 GLN B 388 ASN B 613 GLN B 787 GLN B 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135158 restraints weight = 48223.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132326 restraints weight = 59284.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134038 restraints weight = 45928.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134642 restraints weight = 31626.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134876 restraints weight = 28993.784| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27399 Z= 0.136 Angle : 0.694 14.391 37384 Z= 0.330 Chirality : 0.050 0.401 4343 Planarity : 0.004 0.070 4754 Dihedral : 4.825 25.200 3570 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.93 % Allowed : 6.41 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.14), residues: 3291 helix: -0.55 (0.21), residues: 611 sheet: -0.58 (0.21), residues: 597 loop : -1.86 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.026 0.001 TYR C1138 PHE 0.024 0.001 PHE A 92 TRP 0.027 0.002 TRP B 353 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (27321) covalent geometry : angle 0.66591 / 0.32 (37177) SS BOND : bond 0.00375 / 0.26 ( 27) SS BOND : angle 1.30336 / 0.88 ( 54) hydrogen bonds : bond 0.05540 / 3.67 ( 719) hydrogen bonds : angle 6.90902 / 4.81 ( 1935) link_BETA1-4 : bond 0.00954 / 0.62 ( 18) link_BETA1-4 : angle 1.81128 / 1.18 ( 54) link_NAG-ASN : bond 0.00656 / 0.45 ( 33) link_NAG-ASN : angle 3.54027 / 2.23 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 449 TYR cc_start: 0.6204 (m-80) cc_final: 0.4747 (p90) REVERT: C 869 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7506 (ttm) REVERT: C 1029 MET cc_start: 0.9220 (tpp) cc_final: 0.8660 (ttt) REVERT: C 1041 ASP cc_start: 0.8392 (t0) cc_final: 0.8138 (t0) REVERT: A 386 LYS cc_start: 0.7735 (mttt) cc_final: 0.7525 (mptt) REVERT: A 400 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: B 118 LEU cc_start: 0.7976 (mm) cc_final: 0.7578 (tp) REVERT: B 705 VAL cc_start: 0.7324 (t) cc_final: 0.7086 (t) outliers start: 27 outliers final: 15 residues processed: 288 average time/residue: 0.1771 time to fit residues: 83.4811 Evaluate side-chains 252 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 244 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 448 ASN C 655 HIS C 804 GLN C 901 GLN C 955 ASN C1101 HIS ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131646 restraints weight = 48166.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128013 restraints weight = 59806.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129781 restraints weight = 46185.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130160 restraints weight = 33227.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130322 restraints weight = 30967.469| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27399 Z= 0.173 Angle : 0.691 13.061 37384 Z= 0.328 Chirality : 0.050 0.405 4343 Planarity : 0.004 0.048 4754 Dihedral : 4.913 25.485 3570 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.34 % Allowed : 9.76 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.95 (0.14), residues: 3291 helix: -0.23 (0.21), residues: 606 sheet: -0.73 (0.21), residues: 614 loop : -1.90 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.026 0.002 TYR C 904 PHE 0.031 0.002 PHE A 92 TRP 0.036 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (27321) covalent geometry : angle 0.66477 / 0.32 (37177) SS BOND : bond 0.00439 / 0.31 ( 27) SS BOND : angle 1.32061 / 0.90 ( 54) hydrogen bonds : bond 0.04754 / 3.13 ( 719) hydrogen bonds : angle 6.32244 / 4.39 ( 1935) link_BETA1-4 : bond 0.00776 / 0.53 ( 18) link_BETA1-4 : angle 1.87402 / 1.21 ( 54) link_NAG-ASN : bond 0.00627 / 0.43 ( 33) link_NAG-ASN : angle 3.41963 / 2.17 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9376 (tpp) cc_final: 0.8857 (ttt) REVERT: B 92 PHE cc_start: 0.6189 (m-10) cc_final: 0.5940 (m-10) outliers start: 39 outliers final: 23 residues processed: 269 average time/residue: 0.1752 time to fit residues: 77.3620 Evaluate side-chains 250 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 753 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 211 optimal weight: 0.7980 chunk 262 optimal weight: 0.0570 chunk 135 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 195 optimal weight: 0.3980 chunk 42 optimal weight: 0.0370 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 0.0970 chunk 143 optimal weight: 7.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.170740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136996 restraints weight = 47812.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136438 restraints weight = 82790.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137899 restraints weight = 64305.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139952 restraints weight = 38769.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140147 restraints weight = 33433.104| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27399 Z= 0.106 Angle : 0.637 11.555 37384 Z= 0.299 Chirality : 0.049 0.384 4343 Planarity : 0.004 0.047 4754 Dihedral : 4.662 25.862 3570 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.45 % Allowed : 11.20 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.74 (0.14), residues: 3291 helix: 0.21 (0.22), residues: 609 sheet: -0.52 (0.21), residues: 583 loop : -1.87 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.022 0.001 TYR A 265 PHE 0.030 0.001 PHE A 92 TRP 0.041 0.001 TRP B 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (27321) covalent geometry : angle 0.61166 / 0.29 (37177) SS BOND : bond 0.00253 / 0.16 ( 27) SS BOND : angle 0.98722 / 0.67 ( 54) hydrogen bonds : bond 0.03664 / 2.42 ( 719) hydrogen bonds : angle 5.83023 / 4.05 ( 1935) link_BETA1-4 : bond 0.00805 / 0.54 ( 18) link_BETA1-4 : angle 1.81411 / 1.16 ( 54) link_NAG-ASN : bond 0.00648 / 0.46 ( 33) link_NAG-ASN : angle 3.19085 / 2.04 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.6752 (mttt) cc_final: 0.6518 (tttt) REVERT: C 1041 ASP cc_start: 0.8435 (t0) cc_final: 0.8083 (t0) REVERT: C 1072 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: B 84 LEU cc_start: 0.4507 (OUTLIER) cc_final: 0.4268 (mt) REVERT: B 900 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7908 (mtp) outliers start: 42 outliers final: 21 residues processed: 306 average time/residue: 0.1665 time to fit residues: 85.6046 Evaluate side-chains 259 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 900 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 40 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 289 optimal weight: 0.0570 chunk 230 optimal weight: 30.0000 chunk 71 optimal weight: 0.1980 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 0.0970 chunk 228 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 overall best weight: 1.0298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138799 restraints weight = 47764.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138577 restraints weight = 95558.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140123 restraints weight = 71182.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141243 restraints weight = 42335.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141839 restraints weight = 36316.896| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27399 Z= 0.113 Angle : 0.632 14.296 37384 Z= 0.297 Chirality : 0.049 0.385 4343 Planarity : 0.004 0.055 4754 Dihedral : 4.617 25.945 3570 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.96 % Allowed : 11.79 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.69 (0.14), residues: 3291 helix: 0.28 (0.22), residues: 619 sheet: -0.47 (0.21), residues: 590 loop : -1.85 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.018 0.001 TYR A 265 PHE 0.023 0.001 PHE A 92 TRP 0.043 0.002 TRP B 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (27321) covalent geometry : angle 0.60754 / 0.29 (37177) SS BOND : bond 0.00278 / 0.19 ( 27) SS BOND : angle 0.98223 / 0.68 ( 54) hydrogen bonds : bond 0.03550 / 2.35 ( 719) hydrogen bonds : angle 5.66577 / 3.93 ( 1935) link_BETA1-4 : bond 0.00793 / 0.53 ( 18) link_BETA1-4 : angle 1.80437 / 1.16 ( 54) link_NAG-ASN : bond 0.00582 / 0.41 ( 33) link_NAG-ASN : angle 3.12185 / 2.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1041 ASP cc_start: 0.8501 (t0) cc_final: 0.8106 (t0) REVERT: C 1072 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: A 63 THR cc_start: 0.6818 (OUTLIER) cc_final: 0.6337 (p) REVERT: A 451 TYR cc_start: 0.4419 (m-10) cc_final: 0.4100 (m-80) REVERT: A 1054 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (mm-40) outliers start: 57 outliers final: 28 residues processed: 291 average time/residue: 0.1655 time to fit residues: 79.5326 Evaluate side-chains 268 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 753 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 264 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 320 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 644 GLN B1010 GLN B1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.167425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137399 restraints weight = 47714.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139058 restraints weight = 108481.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139679 restraints weight = 61102.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140440 restraints weight = 39821.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140937 restraints weight = 33743.474| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27399 Z= 0.157 Angle : 0.660 14.373 37384 Z= 0.311 Chirality : 0.049 0.386 4343 Planarity : 0.004 0.056 4754 Dihedral : 4.715 26.278 3570 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.90 % Allowed : 13.10 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.75 (0.14), residues: 3291 helix: 0.28 (0.22), residues: 615 sheet: -0.53 (0.21), residues: 586 loop : -1.90 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.025 0.002 TYR A 265 PHE 0.025 0.002 PHE A 92 TRP 0.048 0.002 TRP C 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (27321) covalent geometry : angle 0.63674 / 0.31 (37177) SS BOND : bond 0.00376 / 0.27 ( 27) SS BOND : angle 1.31275 / 0.92 ( 54) hydrogen bonds : bond 0.03755 / 2.47 ( 719) hydrogen bonds : angle 5.63503 / 3.90 ( 1935) link_BETA1-4 : bond 0.00760 / 0.51 ( 18) link_BETA1-4 : angle 1.82913 / 1.17 ( 54) link_NAG-ASN : bond 0.00558 / 0.39 ( 33) link_NAG-ASN : angle 3.09561 / 2.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1041 ASP cc_start: 0.8548 (t0) cc_final: 0.8121 (t0) REVERT: A 63 THR cc_start: 0.6833 (OUTLIER) cc_final: 0.6367 (p) REVERT: B 104 TRP cc_start: 0.6835 (m100) cc_final: 0.6326 (m100) REVERT: B 644 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6422 (tm130) outliers start: 55 outliers final: 38 residues processed: 273 average time/residue: 0.1730 time to fit residues: 77.8575 Evaluate side-chains 268 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 94 optimal weight: 7.9990 chunk 315 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 165 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 230 optimal weight: 30.0000 chunk 278 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 287 optimal weight: 0.0980 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136222 restraints weight = 47566.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138001 restraints weight = 107710.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138620 restraints weight = 58040.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139372 restraints weight = 38560.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139833 restraints weight = 32960.997| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27399 Z= 0.166 Angle : 0.669 15.038 37384 Z= 0.317 Chirality : 0.050 0.397 4343 Planarity : 0.004 0.057 4754 Dihedral : 4.818 25.985 3570 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.93 % Allowed : 14.06 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.77 (0.14), residues: 3291 helix: 0.32 (0.22), residues: 608 sheet: -0.61 (0.21), residues: 591 loop : -1.91 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 646 TYR 0.025 0.002 TYR A 265 PHE 0.029 0.002 PHE B 643 TRP 0.045 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (27321) covalent geometry : angle 0.64452 / 0.31 (37177) SS BOND : bond 0.00416 / 0.30 ( 27) SS BOND : angle 1.72342 / 1.12 ( 54) hydrogen bonds : bond 0.03820 / 2.51 ( 719) hydrogen bonds : angle 5.64922 / 3.90 ( 1935) link_BETA1-4 : bond 0.00766 / 0.52 ( 18) link_BETA1-4 : angle 1.83750 / 1.18 ( 54) link_NAG-ASN : bond 0.00558 / 0.39 ( 33) link_NAG-ASN : angle 3.11450 / 2.02 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 104 TRP cc_start: 0.6978 (m100) cc_final: 0.6506 (m100) outliers start: 56 outliers final: 41 residues processed: 266 average time/residue: 0.1664 time to fit residues: 73.7845 Evaluate side-chains 266 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 94 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN B 188 ASN B 207 HIS B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134401 restraints weight = 47646.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135693 restraints weight = 105379.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136997 restraints weight = 68406.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136896 restraints weight = 48202.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139051 restraints weight = 37332.319| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27399 Z= 0.164 Angle : 0.675 14.816 37384 Z= 0.319 Chirality : 0.050 0.368 4343 Planarity : 0.004 0.056 4754 Dihedral : 4.900 26.819 3570 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.14 % Allowed : 14.24 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.82 (0.14), residues: 3291 helix: 0.32 (0.22), residues: 609 sheet: -0.76 (0.20), residues: 617 loop : -1.93 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.025 0.002 TYR C 904 PHE 0.028 0.002 PHE A 92 TRP 0.048 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (27321) covalent geometry : angle 0.65096 / 0.31 (37177) SS BOND : bond 0.00401 / 0.29 ( 27) SS BOND : angle 1.38691 / 0.94 ( 54) hydrogen bonds : bond 0.03816 / 2.52 ( 719) hydrogen bonds : angle 5.61702 / 3.88 ( 1935) link_BETA1-4 : bond 0.00758 / 0.52 ( 18) link_BETA1-4 : angle 1.83897 / 1.18 ( 54) link_NAG-ASN : bond 0.00533 / 0.37 ( 33) link_NAG-ASN : angle 3.15590 / 2.09 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.5434 (tpp) cc_final: 0.5169 (tpp) REVERT: A 303 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 104 TRP cc_start: 0.7097 (m100) cc_final: 0.6675 (m100) REVERT: B 171 VAL cc_start: 0.7729 (t) cc_final: 0.7102 (p) REVERT: B 188 ASN cc_start: 0.6001 (OUTLIER) cc_final: 0.4509 (t0) outliers start: 62 outliers final: 45 residues processed: 279 average time/residue: 0.1615 time to fit residues: 74.3852 Evaluate side-chains 271 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 151 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 273 optimal weight: 0.0000 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.0070 chunk 242 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 overall best weight: 2.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134987 restraints weight = 47543.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136744 restraints weight = 111031.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137439 restraints weight = 60063.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138439 restraints weight = 39056.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138841 restraints weight = 32453.326| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27399 Z= 0.168 Angle : 0.681 16.804 37384 Z= 0.322 Chirality : 0.050 0.365 4343 Planarity : 0.004 0.060 4754 Dihedral : 4.970 27.980 3570 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.10 % Allowed : 14.37 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.84 (0.14), residues: 3291 helix: 0.33 (0.22), residues: 609 sheet: -0.77 (0.21), residues: 617 loop : -1.95 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.025 0.002 TYR B1007 PHE 0.043 0.002 PHE B 186 TRP 0.029 0.002 TRP C 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (27321) covalent geometry : angle 0.65784 / 0.32 (37177) SS BOND : bond 0.00401 / 0.29 ( 27) SS BOND : angle 1.37123 / 0.92 ( 54) hydrogen bonds : bond 0.03834 / 2.53 ( 719) hydrogen bonds : angle 5.62293 / 3.88 ( 1935) link_BETA1-4 : bond 0.00744 / 0.51 ( 18) link_BETA1-4 : angle 1.85127 / 1.19 ( 54) link_NAG-ASN : bond 0.00550 / 0.38 ( 33) link_NAG-ASN : angle 3.12902 / 2.06 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 231 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7543 (t80) cc_final: 0.7283 (t80) REVERT: A 303 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8524 (mp) REVERT: B 104 TRP cc_start: 0.7104 (m100) cc_final: 0.6798 (m100) REVERT: B 171 VAL cc_start: 0.7680 (t) cc_final: 0.7057 (p) REVERT: B 188 ASN cc_start: 0.6246 (OUTLIER) cc_final: 0.4713 (t0) outliers start: 61 outliers final: 49 residues processed: 274 average time/residue: 0.1571 time to fit residues: 71.5477 Evaluate side-chains 279 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 306 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 271 optimal weight: 0.0050 chunk 162 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 238 optimal weight: 40.0000 chunk 200 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.166599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131119 restraints weight = 47422.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129064 restraints weight = 59796.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130170 restraints weight = 51864.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130880 restraints weight = 35554.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131299 restraints weight = 31524.852| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27399 Z= 0.128 Angle : 0.658 15.834 37384 Z= 0.312 Chirality : 0.049 0.363 4343 Planarity : 0.004 0.060 4754 Dihedral : 4.890 27.823 3570 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.83 % Allowed : 15.10 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.72 (0.14), residues: 3291 helix: 0.48 (0.22), residues: 608 sheet: -0.65 (0.21), residues: 585 loop : -1.90 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.039 0.001 TYR B 160 PHE 0.032 0.001 PHE A 429 TRP 0.043 0.002 TRP B 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (27321) covalent geometry : angle 0.63699 / 0.31 (37177) SS BOND : bond 0.00355 / 0.26 ( 27) SS BOND : angle 1.35225 / 0.94 ( 54) hydrogen bonds : bond 0.03552 / 2.35 ( 719) hydrogen bonds : angle 5.50622 / 3.79 ( 1935) link_BETA1-4 : bond 0.00744 / 0.50 ( 18) link_BETA1-4 : angle 1.82579 / 1.17 ( 54) link_NAG-ASN : bond 0.00533 / 0.37 ( 33) link_NAG-ASN : angle 2.90821 / 1.90 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 104 TRP cc_start: 0.7145 (m100) cc_final: 0.6638 (m100) REVERT: B 118 LEU cc_start: 0.7997 (mm) cc_final: 0.7648 (tp) REVERT: B 171 VAL cc_start: 0.7857 (t) cc_final: 0.7224 (p) outliers start: 53 outliers final: 45 residues processed: 276 average time/residue: 0.1484 time to fit residues: 68.2354 Evaluate side-chains 278 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 79 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 226 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 111 optimal weight: 0.3980 chunk 263 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 309 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.167377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136206 restraints weight = 47248.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137823 restraints weight = 96411.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138724 restraints weight = 64585.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138553 restraints weight = 48176.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140315 restraints weight = 37339.855| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27399 Z= 0.114 Angle : 0.638 16.434 37384 Z= 0.302 Chirality : 0.048 0.361 4343 Planarity : 0.004 0.061 4754 Dihedral : 4.771 26.819 3570 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.62 % Allowed : 15.31 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.64 (0.14), residues: 3291 helix: 0.59 (0.22), residues: 616 sheet: -0.60 (0.21), residues: 571 loop : -1.85 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.019 0.001 TYR B1007 PHE 0.030 0.001 PHE A 429 TRP 0.033 0.002 TRP B 353 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (27321) covalent geometry : angle 0.61860 / 0.30 (37177) SS BOND : bond 0.00291 / 0.20 ( 27) SS BOND : angle 1.14946 / 0.79 ( 54) hydrogen bonds : bond 0.03345 / 2.23 ( 719) hydrogen bonds : angle 5.36812 / 3.69 ( 1935) link_BETA1-4 : bond 0.00781 / 0.53 ( 18) link_BETA1-4 : angle 1.80523 / 1.16 ( 54) link_NAG-ASN : bond 0.00510 / 0.35 ( 33) link_NAG-ASN : angle 2.72849 / 1.81 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.98 seconds wall clock time: 67 minutes 0.21 seconds (4020.21 seconds total)