Starting phenix.real_space_refine on Wed Jun 25 05:11:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_32038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_32038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_32038.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_32038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnc_32038/06_2025/7vnc_32038.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.35s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 27 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.46, per 1000 atoms: 0.58 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: 7.54 Conformation dependent library (CDL) restraints added in 4.0 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: 3.78 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: 10.88 Time building geometry restraints manager: 8.69 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 - 23.13: 15504 23.13 - 46.26: 1073 46.26 - 69.39: 158 69.39 - 92.52: 88 92.52 - 115.65: 55 Dihedral angle restraints: 16878 sinusoidal: 7209 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 16875 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 1146 or resid 1301 thr \ ough 1303)) selection = (chain 'B' and (resid 14 through 1146 or resid 1301 through 1303)) selection = (chain 'C' and (resid 14 through 334 or resid 336 through 1146 or resid 1301 thr \ ough 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 62.630 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 18.012 115.654 10585 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.002 TRP C 353 HIS 0.007 0.001 HIS C 49 PHE 0.023 0.001 PHE C 377 TYR 0.023 0.001 TYR B 351 ARG 0.007 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 33) link_NAG-ASN : angle 3.60228 ( 99) link_BETA1-4 : bond 0.00536 ( 18) link_BETA1-4 : angle 1.53951 ( 54) hydrogen bonds : bond 0.29487 ( 719) hydrogen bonds : angle 10.32058 ( 1935) SS BOND : bond 0.00288 ( 27) SS BOND : angle 1.37945 ( 54) covalent geometry : bond 0.00905 (27321) covalent geometry : angle 0.76633 (37177) *********************** 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 : 2.860 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: 0.8688 (ttt) REVERT: B 358 ILE cc_start: 0.8387 (mt) cc_final: 0.8175 (tt) REVERT: B 454 ARG cc_start: 0.6296 (ttt-90) cc_final: 0.6031 (ptm160) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.3483 time to fit residues: 185.5123 Evaluate side-chains 232 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 157 optimal weight: 0.1980 chunk 193 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 448 ASN 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 = 0.4156 r_free = 0.4156 target = 0.170283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134732 restraints weight = 48137.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131555 restraints weight = 58750.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133086 restraints weight = 46970.681| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27399 Z= 0.148 Angle : 0.736 14.261 37384 Z= 0.342 Chirality : 0.050 0.393 4343 Planarity : 0.005 0.068 4754 Dihedral : 14.571 109.400 4641 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.93 % Allowed : 6.79 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3291 helix: -0.60 (0.21), residues: 612 sheet: -0.64 (0.21), residues: 598 loop : -1.87 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 353 HIS 0.009 0.001 HIS C 49 PHE 0.033 0.002 PHE A 927 TYR 0.026 0.002 TYR C1138 ARG 0.006 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 33) link_NAG-ASN : angle 3.72644 ( 99) link_BETA1-4 : bond 0.00775 ( 18) link_BETA1-4 : angle 2.72325 ( 54) hydrogen bonds : bond 0.05319 ( 719) hydrogen bonds : angle 6.84346 ( 1935) SS BOND : bond 0.00404 ( 27) SS BOND : angle 1.37345 ( 54) covalent geometry : bond 0.00343 (27321) covalent geometry : angle 0.70301 (37177) *********************** 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 306 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9277 (tpp) cc_final: 0.8723 (ttt) REVERT: C 1041 ASP cc_start: 0.8465 (t0) cc_final: 0.8192 (t0) REVERT: A 400 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6403 (m-10) REVERT: B 118 LEU cc_start: 0.7953 (mm) cc_final: 0.7559 (tp) REVERT: B 537 LYS cc_start: 0.5792 (ptmm) cc_final: 0.5456 (mttp) REVERT: B 705 VAL cc_start: 0.7525 (t) cc_final: 0.7267 (t) outliers start: 27 outliers final: 16 residues processed: 295 average time/residue: 0.4661 time to fit residues: 227.9814 Evaluate side-chains 250 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 5.159 ------------------------------------------------------------------------------- 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 957 GLN Chi-restraints excluded: chain C residue 1077 THR 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 297 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 182 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133714 restraints weight = 47872.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130957 restraints weight = 57799.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132659 restraints weight = 47063.634| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27399 Z= 0.121 Angle : 0.686 12.654 37384 Z= 0.316 Chirality : 0.048 0.437 4343 Planarity : 0.004 0.049 4754 Dihedral : 12.410 108.927 4641 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.24 % Allowed : 9.93 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3291 helix: -0.10 (0.22), residues: 605 sheet: -0.54 (0.21), residues: 593 loop : -1.88 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 353 HIS 0.006 0.001 HIS C 49 PHE 0.034 0.001 PHE A 92 TYR 0.020 0.001 TYR C1138 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 33) link_NAG-ASN : angle 3.53792 ( 99) link_BETA1-4 : bond 0.00648 ( 18) link_BETA1-4 : angle 2.80339 ( 54) hydrogen bonds : bond 0.04400 ( 719) hydrogen bonds : angle 6.18839 ( 1935) SS BOND : bond 0.00330 ( 27) SS BOND : angle 1.14612 ( 54) covalent geometry : bond 0.00287 (27321) covalent geometry : angle 0.65327 (37177) *********************** 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 290 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1041 ASP cc_start: 0.8541 (t0) cc_final: 0.8210 (t0) REVERT: A 400 PHE cc_start: 0.6612 (m-10) cc_final: 0.6379 (m-10) REVERT: B 565 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5508 (m-80) outliers start: 36 outliers final: 18 residues processed: 278 average time/residue: 0.3357 time to fit residues: 154.9119 Evaluate side-chains 247 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 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 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 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 1105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 30 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 280 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 ASN C 655 HIS C 901 GLN C 955 ASN C 957 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN B 81 ASN ** B 115 GLN ** 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 388 ASN B 409 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.163013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132465 restraints weight = 48062.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133950 restraints weight = 119124.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135263 restraints weight = 62769.789| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27399 Z= 0.260 Angle : 0.802 11.217 37384 Z= 0.380 Chirality : 0.052 0.464 4343 Planarity : 0.005 0.048 4754 Dihedral : 11.803 108.292 4641 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.00 % Allowed : 12.34 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3291 helix: -0.32 (0.21), residues: 616 sheet: -1.01 (0.20), residues: 648 loop : -2.07 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 353 HIS 0.008 0.002 HIS B1058 PHE 0.027 0.002 PHE B 802 TYR 0.045 0.002 TYR B1067 ARG 0.005 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 33) link_NAG-ASN : angle 3.70810 ( 99) link_BETA1-4 : bond 0.00727 ( 18) link_BETA1-4 : angle 3.05678 ( 54) hydrogen bonds : bond 0.04988 ( 719) hydrogen bonds : angle 6.28123 ( 1935) SS BOND : bond 0.00626 ( 27) SS BOND : angle 1.67234 ( 54) covalent geometry : bond 0.00618 (27321) covalent geometry : angle 0.76993 (37177) *********************** 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 302 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1072 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: B 985 ASP cc_start: 0.6932 (t70) cc_final: 0.6627 (t70) outliers start: 58 outliers final: 40 residues processed: 285 average time/residue: 0.3513 time to fit residues: 163.8071 Evaluate side-chains 267 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR 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 305 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 452 LEU 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 740 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 952 VAL 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 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 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU 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 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 chunk 190 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 297 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132574 restraints weight = 47781.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133916 restraints weight = 107872.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134971 restraints weight = 66641.017| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27399 Z= 0.186 Angle : 0.718 11.216 37384 Z= 0.338 Chirality : 0.050 0.416 4343 Planarity : 0.004 0.049 4754 Dihedral : 11.329 105.162 4641 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.41 % Allowed : 13.62 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3291 helix: -0.07 (0.22), residues: 607 sheet: -0.94 (0.21), residues: 621 loop : -2.05 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 PHE 0.026 0.002 PHE B 86 TYR 0.030 0.002 TYR A 265 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 33) link_NAG-ASN : angle 3.54836 ( 99) link_BETA1-4 : bond 0.00687 ( 18) link_BETA1-4 : angle 3.06335 ( 54) hydrogen bonds : bond 0.04264 ( 719) hydrogen bonds : angle 6.03613 ( 1935) SS BOND : bond 0.00445 ( 27) SS BOND : angle 1.37691 ( 54) covalent geometry : bond 0.00445 (27321) covalent geometry : angle 0.68498 (37177) *********************** 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 308 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1072 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: B 543 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: B 644 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.6659 (tm130) outliers start: 70 outliers final: 41 residues processed: 287 average time/residue: 0.3544 time to fit residues: 167.4852 Evaluate side-chains 259 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 SER 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 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 1072 GLU 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 400 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 770 ILE Chi-restraints excluded: chain A residue 952 VAL 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 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 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 543 PHE 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 644 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 24 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 250 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 56 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133333 restraints weight = 47712.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134773 restraints weight = 107627.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136045 restraints weight = 68549.001| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27399 Z= 0.167 Angle : 0.709 11.415 37384 Z= 0.331 Chirality : 0.049 0.415 4343 Planarity : 0.004 0.049 4754 Dihedral : 10.988 103.968 4641 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.24 % Allowed : 14.62 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3291 helix: 0.02 (0.22), residues: 609 sheet: -0.97 (0.20), residues: 634 loop : -2.03 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 PHE 0.022 0.002 PHE B 186 TYR 0.025 0.002 TYR B1067 ARG 0.004 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 33) link_NAG-ASN : angle 3.48475 ( 99) link_BETA1-4 : bond 0.00703 ( 18) link_BETA1-4 : angle 3.04644 ( 54) hydrogen bonds : bond 0.04039 ( 719) hydrogen bonds : angle 5.90356 ( 1935) SS BOND : bond 0.00597 ( 27) SS BOND : angle 1.52048 ( 54) covalent geometry : bond 0.00401 (27321) covalent geometry : angle 0.67586 (37177) *********************** 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 301 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 581 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7231 (p) REVERT: C 1072 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: B 985 ASP cc_start: 0.7154 (t70) cc_final: 0.6754 (t70) REVERT: B 1111 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6977 (tp30) outliers start: 65 outliers final: 50 residues processed: 283 average time/residue: 0.3802 time to fit residues: 178.3092 Evaluate side-chains 276 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 SER 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 289 VAL Chi-restraints excluded: chain C residue 581 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 895 GLN 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 1072 GLU Chi-restraints excluded: chain C residue 1077 THR 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 400 PHE 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 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 990 GLU 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 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU 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 Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 250 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132987 restraints weight = 47681.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134492 restraints weight = 104289.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135382 restraints weight = 66401.116| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27399 Z= 0.157 Angle : 0.700 11.751 37384 Z= 0.327 Chirality : 0.049 0.409 4343 Planarity : 0.004 0.049 4754 Dihedral : 10.645 103.719 4641 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.55 % Allowed : 15.31 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3291 helix: 0.10 (0.22), residues: 615 sheet: -0.82 (0.21), residues: 611 loop : -2.03 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 353 HIS 0.005 0.001 HIS C 49 PHE 0.034 0.002 PHE B 86 TYR 0.027 0.002 TYR A 453 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 33) link_NAG-ASN : angle 3.36399 ( 99) link_BETA1-4 : bond 0.00641 ( 18) link_BETA1-4 : angle 3.00303 ( 54) hydrogen bonds : bond 0.03860 ( 719) hydrogen bonds : angle 5.78844 ( 1935) SS BOND : bond 0.00511 ( 27) SS BOND : angle 1.67400 ( 54) covalent geometry : bond 0.00376 (27321) covalent geometry : angle 0.66729 (37177) *********************** 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 305 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ILE cc_start: 0.2669 (OUTLIER) cc_final: 0.2297 (pt) REVERT: C 1072 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: A 303 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 171 VAL cc_start: 0.7704 (t) cc_final: 0.7068 (p) REVERT: B 985 ASP cc_start: 0.7205 (t70) cc_final: 0.6810 (t70) outliers start: 74 outliers final: 55 residues processed: 286 average time/residue: 0.3391 time to fit residues: 161.2827 Evaluate side-chains 279 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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 68 ILE 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 289 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 SER 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 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 990 GLU 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 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU 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 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 0.0870 chunk 301 optimal weight: 2.9990 chunk 221 optimal weight: 0.0010 chunk 273 optimal weight: 0.0970 chunk 306 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.6366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN B 188 ASN B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.165492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134265 restraints weight = 47758.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135625 restraints weight = 101275.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136934 restraints weight = 68353.210| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27399 Z= 0.129 Angle : 0.681 11.801 37384 Z= 0.318 Chirality : 0.048 0.406 4343 Planarity : 0.004 0.049 4754 Dihedral : 10.290 103.848 4641 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.41 % Allowed : 15.79 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3291 helix: 0.28 (0.22), residues: 610 sheet: -0.77 (0.21), residues: 602 loop : -1.98 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 353 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.001 PHE B 186 TYR 0.027 0.001 TYR B 160 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 33) link_NAG-ASN : angle 3.29502 ( 99) link_BETA1-4 : bond 0.00648 ( 18) link_BETA1-4 : angle 2.98990 ( 54) hydrogen bonds : bond 0.03618 ( 719) hydrogen bonds : angle 5.66262 ( 1935) SS BOND : bond 0.00433 ( 27) SS BOND : angle 1.67287 ( 54) covalent geometry : bond 0.00312 (27321) covalent geometry : angle 0.64833 (37177) *********************** 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 310 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1072 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: A 303 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 171 VAL cc_start: 0.7704 (t) cc_final: 0.7062 (p) REVERT: B 188 ASN cc_start: 0.5883 (OUTLIER) cc_final: 0.4246 (t0) REVERT: B 985 ASP cc_start: 0.7238 (t70) cc_final: 0.6876 (t70) outliers start: 70 outliers final: 58 residues processed: 291 average time/residue: 0.3595 time to fit residues: 173.4962 Evaluate side-chains 291 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR 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 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN 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 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 130 VAL 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 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 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 990 GLU Chi-restraints excluded: chain A residue 991 VAL 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 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU 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 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 242 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 328 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN B 188 ASN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.165058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132027 restraints weight = 47857.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133179 restraints weight = 94821.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134918 restraints weight = 62148.486| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27399 Z= 0.139 Angle : 0.685 11.637 37384 Z= 0.320 Chirality : 0.048 0.402 4343 Planarity : 0.004 0.049 4754 Dihedral : 9.956 103.920 4641 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.52 % Allowed : 15.96 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3291 helix: 0.32 (0.22), residues: 609 sheet: -0.80 (0.21), residues: 605 loop : -1.95 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 353 HIS 0.004 0.001 HIS C 49 PHE 0.025 0.002 PHE C 400 TYR 0.022 0.001 TYR A 453 ARG 0.006 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 33) link_NAG-ASN : angle 3.33319 ( 99) link_BETA1-4 : bond 0.00665 ( 18) link_BETA1-4 : angle 3.00385 ( 54) hydrogen bonds : bond 0.03636 ( 719) hydrogen bonds : angle 5.61296 ( 1935) SS BOND : bond 0.00464 ( 27) SS BOND : angle 1.35758 ( 54) covalent geometry : bond 0.00336 (27321) covalent geometry : angle 0.65341 (37177) *********************** 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 310 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.4604 (OUTLIER) cc_final: 0.3981 (m) REVERT: A 303 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 171 VAL cc_start: 0.7798 (t) cc_final: 0.7164 (p) REVERT: B 188 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.4336 (t0) REVERT: B 985 ASP cc_start: 0.7385 (t70) cc_final: 0.6977 (t70) outliers start: 73 outliers final: 60 residues processed: 292 average time/residue: 0.3458 time to fit residues: 167.6018 Evaluate side-chains 294 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR 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 289 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 610 VAL 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 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN 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 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS 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 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 906 PHE Chi-restraints excluded: chain A residue 916 LEU 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 990 GLU 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 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU 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 Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 309 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 317 ASN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129394 restraints weight = 47583.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121227 restraints weight = 53145.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120887 restraints weight = 48826.969| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27399 Z= 0.208 Angle : 0.739 10.401 37384 Z= 0.349 Chirality : 0.050 0.393 4343 Planarity : 0.004 0.049 4754 Dihedral : 9.872 105.188 4641 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.41 % Allowed : 16.48 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3291 helix: 0.14 (0.22), residues: 609 sheet: -1.03 (0.20), residues: 644 loop : -2.01 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 104 HIS 0.007 0.001 HIS C 49 PHE 0.024 0.002 PHE B 133 TYR 0.034 0.002 TYR B1067 ARG 0.006 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 33) link_NAG-ASN : angle 3.51358 ( 99) link_BETA1-4 : bond 0.00703 ( 18) link_BETA1-4 : angle 3.04017 ( 54) hydrogen bonds : bond 0.04130 ( 719) hydrogen bonds : angle 5.76621 ( 1935) SS BOND : bond 0.00538 ( 27) SS BOND : angle 1.61217 ( 54) covalent geometry : bond 0.00498 (27321) covalent geometry : angle 0.70676 (37177) ********************** 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 297 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 3.184 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.4521 (OUTLIER) cc_final: 0.3967 (m) REVERT: A 303 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 171 VAL cc_start: 0.8084 (t) cc_final: 0.7489 (p) outliers start: 70 outliers final: 61 residues processed: 280 average time/residue: 0.3652 time to fit residues: 167.4655 Evaluate side-chains 283 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR 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 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN 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 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS 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 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 649 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1030 SER 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 305 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU 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 Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 276 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 273 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 134 GLN B 317 ASN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133193 restraints weight = 47552.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132741 restraints weight = 81154.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134081 restraints weight = 64674.324| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27399 Z= 0.109 Angle : 0.668 10.704 37384 Z= 0.315 Chirality : 0.047 0.407 4343 Planarity : 0.004 0.049 4754 Dihedral : 9.459 105.354 4641 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.86 % Allowed : 16.99 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3291 helix: 0.49 (0.22), residues: 611 sheet: -0.74 (0.21), residues: 605 loop : -1.90 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 353 HIS 0.010 0.001 HIS C 49 PHE 0.036 0.001 PHE A 133 TYR 0.030 0.001 TYR B 160 ARG 0.007 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 33) link_NAG-ASN : angle 3.22591 ( 99) link_BETA1-4 : bond 0.00649 ( 18) link_BETA1-4 : angle 2.86995 ( 54) hydrogen bonds : bond 0.03337 ( 719) hydrogen bonds : angle 5.48067 ( 1935) SS BOND : bond 0.00332 ( 27) SS BOND : angle 1.37062 ( 54) covalent geometry : bond 0.00260 (27321) covalent geometry : angle 0.63739 (37177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7518.54 seconds wall clock time: 133 minutes 34.25 seconds (8014.25 seconds total)