Starting phenix.real_space_refine on Thu Mar 5 22:54:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgx_32491/03_2026/7wgx_32491.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16329 2.51 5 N 4182 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25629 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "B" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "C" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.60, per 1000 atoms: 0.22 Number of scatterers: 25629 At special positions: 0 Unit cell: (139.05, 133.65, 179.55, 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 117 16.00 O 5001 8.00 N 4182 7.00 C 16329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 61 " " NAG A1604 " - " ASN A 616 " " NAG A1605 " - " ASN A1134 " " NAG A1606 " - " ASN A 282 " " NAG A1607 " - " ASN A 709 " " NAG A1608 " - " ASN A 165 " " NAG A1609 " - " ASN A1074 " " NAG B1601 " - " ASN B 343 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 61 " " NAG B1604 " - " ASN B 616 " " NAG B1605 " - " ASN B1134 " " NAG B1606 " - " ASN B 282 " " NAG B1607 " - " ASN B 709 " " NAG B1608 " - " ASN B 165 " " NAG B1609 " - " ASN B1074 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 61 " " NAG C1604 " - " ASN C 616 " " NAG C1605 " - " ASN C1134 " " NAG C1606 " - " ASN C 282 " " NAG C1607 " - " ASN C 709 " " NAG C1608 " - " ASN C 165 " " NAG C1609 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 122 " " NAG R 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 754.6 milliseconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 26.4% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.520A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.322A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.150A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.637A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (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 984 removed outlier: 3.575A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.913A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.520A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.320A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.177A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.659A 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 758 through 783 removed outlier: 3.501A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.149A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.575A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.913A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.521A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.322A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.659A 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: 3.502A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.150A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (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: 3.575A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.914A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.019A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.663A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.751A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.771A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.310A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.371A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.455A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.875A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.472A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.018A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.751A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.769A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.310A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.036A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.372A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.456A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.885A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.019A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.752A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.770A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.036A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.372A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.456A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.33: 7146 1.33 - 1.51: 9211 1.51 - 1.69: 9656 1.69 - 1.88: 165 1.88 - 2.06: 9 Bond restraints: 26187 Sorted by residual: bond pdb=" C1A BLR C1610 " pdb=" CHA BLR C1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.79e+02 bond pdb=" C1A BLR A1610 " pdb=" CHA BLR A1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.78e+02 bond pdb=" C1A BLR B1610 " pdb=" CHA BLR B1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.77e+02 bond pdb=" C2B BLR C1610 " pdb=" CMB BLR C1610 " ideal model delta sigma weight residual 1.489 1.954 -0.465 2.00e-02 2.50e+03 5.40e+02 bond pdb=" C2B BLR B1610 " pdb=" CMB BLR B1610 " ideal model delta sigma weight residual 1.489 1.954 -0.465 2.00e-02 2.50e+03 5.40e+02 ... (remaining 26182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.38: 35595 9.38 - 18.76: 9 18.76 - 28.13: 3 28.13 - 37.51: 6 37.51 - 46.89: 12 Bond angle restraints: 35625 Sorted by residual: angle pdb=" C2B BLR B1610 " pdb=" C1B BLR B1610 " pdb=" CHB BLR B1610 " ideal model delta sigma weight residual 123.24 170.13 -46.89 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C2B BLR A1610 " pdb=" C1B BLR A1610 " pdb=" CHB BLR A1610 " ideal model delta sigma weight residual 123.24 170.07 -46.83 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C2B BLR C1610 " pdb=" C1B BLR C1610 " pdb=" CHB BLR C1610 " ideal model delta sigma weight residual 123.24 170.06 -46.82 3.00e+00 1.11e-01 2.44e+02 angle pdb=" NB BLR B1610 " pdb=" C1B BLR B1610 " pdb=" CHB BLR B1610 " ideal model delta sigma weight residual 130.12 88.81 41.31 3.00e+00 1.11e-01 1.90e+02 angle pdb=" NB BLR A1610 " pdb=" C1B BLR A1610 " pdb=" CHB BLR A1610 " ideal model delta sigma weight residual 130.12 88.82 41.30 3.00e+00 1.11e-01 1.90e+02 ... (remaining 35620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15013 17.97 - 35.94: 995 35.94 - 53.91: 213 53.91 - 71.89: 54 71.89 - 89.86: 39 Dihedral angle restraints: 16314 sinusoidal: 7107 harmonic: 9207 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.03 74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.03 74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 16311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3320 0.051 - 0.102: 626 0.102 - 0.153: 227 0.153 - 0.205: 15 0.205 - 0.256: 6 Chirality restraints: 4194 Sorted by residual: chirality pdb=" CA LYS A 795 " pdb=" N LYS A 795 " pdb=" C LYS A 795 " pdb=" CB LYS A 795 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS C 795 " pdb=" N LYS C 795 " pdb=" C LYS C 795 " pdb=" CB LYS C 795 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LYS B 795 " pdb=" N LYS B 795 " pdb=" C LYS B 795 " pdb=" CB LYS B 795 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4191 not shown) Planarity restraints: 4575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO C 621 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 621 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 621 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.063 5.00e-02 4.00e+02 ... (remaining 4572 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 5424 2.78 - 3.31: 22971 3.31 - 3.84: 39599 3.84 - 4.37: 45774 4.37 - 4.90: 82618 Nonbonded interactions: 196386 Sorted by model distance: nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 191 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.281 3.040 ... (remaining 196381 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.980 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.017 0.558 26289 Z= 0.875 Angle : 1.203 46.890 35880 Z= 0.451 Chirality : 0.047 0.256 4194 Planarity : 0.005 0.118 4533 Dihedral : 13.506 89.857 10260 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.95 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3117 helix: 0.96 (0.22), residues: 654 sheet: 0.95 (0.18), residues: 744 loop : -0.91 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.014 0.001 TYR C1067 PHE 0.010 0.001 PHE C 133 TRP 0.009 0.001 TRP A 64 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.01743 (26187) covalent geometry : angle 1.19728 (35625) SS BOND : bond 0.00198 ( 42) SS BOND : angle 0.97612 ( 84) hydrogen bonds : bond 0.11537 ( 994) hydrogen bonds : angle 6.07389 ( 2829) Misc. bond : bond 0.09463 ( 3) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 0.52161 ( 45) link_NAG-ASN : bond 0.00390 ( 42) link_NAG-ASN : angle 2.40249 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.922 Fit side-chains REVERT: A 606 ASN cc_start: 0.8206 (t0) cc_final: 0.7996 (t0) REVERT: B 1029 MET cc_start: 0.8715 (tpp) cc_final: 0.8415 (tpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1487 time to fit residues: 41.3710 Evaluate side-chains 110 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1135 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.105900 restraints weight = 46398.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108322 restraints weight = 27742.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109166 restraints weight = 20591.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109479 restraints weight = 17781.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109772 restraints weight = 16906.828| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26289 Z= 0.233 Angle : 0.650 10.301 35880 Z= 0.328 Chirality : 0.048 0.224 4194 Planarity : 0.005 0.119 4533 Dihedral : 8.434 81.195 4626 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.65 % Favored : 94.96 % Rotamer: Outliers : 0.40 % Allowed : 3.53 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3117 helix: 1.15 (0.21), residues: 666 sheet: 0.81 (0.18), residues: 726 loop : -1.08 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.022 0.002 TYR B 904 PHE 0.019 0.002 PHE B 429 TRP 0.011 0.002 TRP B 436 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00562 (26187) covalent geometry : angle 0.63193 (35625) SS BOND : bond 0.00269 ( 42) SS BOND : angle 0.74874 ( 84) hydrogen bonds : bond 0.05885 ( 994) hydrogen bonds : angle 5.09063 ( 2829) Misc. bond : bond 0.00586 ( 3) link_BETA1-4 : bond 0.00437 ( 15) link_BETA1-4 : angle 1.12112 ( 45) link_NAG-ASN : bond 0.00424 ( 42) link_NAG-ASN : angle 2.55792 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.925 Fit side-chains REVERT: A 606 ASN cc_start: 0.8430 (t0) cc_final: 0.8105 (t0) REVERT: C 427 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7637 (t0) REVERT: C 697 MET cc_start: 0.8329 (ptm) cc_final: 0.8119 (ptp) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.1277 time to fit residues: 26.7893 Evaluate side-chains 106 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain C residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104365 restraints weight = 46320.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107381 restraints weight = 29797.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.107965 restraints weight = 20502.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108379 restraints weight = 17531.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108651 restraints weight = 16499.351| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26289 Z= 0.183 Angle : 0.573 8.230 35880 Z= 0.295 Chirality : 0.046 0.199 4194 Planarity : 0.005 0.119 4533 Dihedral : 7.852 76.986 4626 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.30 % Favored : 95.32 % Rotamer: Outliers : 0.58 % Allowed : 5.53 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3117 helix: 1.20 (0.21), residues: 675 sheet: 0.74 (0.18), residues: 726 loop : -1.10 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.018 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00438 (26187) covalent geometry : angle 0.55592 (35625) SS BOND : bond 0.00244 ( 42) SS BOND : angle 0.66652 ( 84) hydrogen bonds : bond 0.05496 ( 994) hydrogen bonds : angle 4.96714 ( 2829) Misc. bond : bond 0.00094 ( 3) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.15019 ( 45) link_NAG-ASN : bond 0.00297 ( 42) link_NAG-ASN : angle 2.33258 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.887 Fit side-chains REVERT: A 606 ASN cc_start: 0.8554 (t0) cc_final: 0.8249 (t0) REVERT: A 933 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8303 (tmtt) REVERT: B 569 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8203 (mp) REVERT: C 957 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7823 (tm-30) outliers start: 16 outliers final: 7 residues processed: 121 average time/residue: 0.1266 time to fit residues: 27.8311 Evaluate side-chains 112 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 271 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 901 GLN B 935 GLN B 955 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.109003 restraints weight = 46002.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111710 restraints weight = 26601.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112519 restraints weight = 18659.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112821 restraints weight = 16316.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113079 restraints weight = 15465.456| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26289 Z= 0.100 Angle : 0.506 10.468 35880 Z= 0.259 Chirality : 0.044 0.198 4194 Planarity : 0.005 0.119 4533 Dihedral : 7.160 72.703 4626 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.27 % Favored : 95.35 % Rotamer: Outliers : 0.44 % Allowed : 7.16 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3117 helix: 1.84 (0.21), residues: 651 sheet: 0.79 (0.18), residues: 735 loop : -0.94 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.017 0.001 TYR A1067 PHE 0.013 0.001 PHE A 65 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00222 (26187) covalent geometry : angle 0.49047 (35625) SS BOND : bond 0.00159 ( 42) SS BOND : angle 0.56403 ( 84) hydrogen bonds : bond 0.04253 ( 994) hydrogen bonds : angle 4.66623 ( 2829) Misc. bond : bond 0.00080 ( 3) link_BETA1-4 : bond 0.00457 ( 15) link_BETA1-4 : angle 1.05142 ( 45) link_NAG-ASN : bond 0.00314 ( 42) link_NAG-ASN : angle 2.06239 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.910 Fit side-chains REVERT: A 606 ASN cc_start: 0.8593 (t0) cc_final: 0.7939 (m-40) REVERT: A 933 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8229 (tmtt) REVERT: A 938 LEU cc_start: 0.7487 (mt) cc_final: 0.7269 (mt) REVERT: B 569 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8174 (mp) REVERT: C 849 LEU cc_start: 0.8576 (mt) cc_final: 0.8358 (mp) outliers start: 12 outliers final: 5 residues processed: 126 average time/residue: 0.1310 time to fit residues: 29.5538 Evaluate side-chains 112 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 299 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103554 restraints weight = 45085.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105643 restraints weight = 29244.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106805 restraints weight = 20806.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108583 restraints weight = 18268.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108846 restraints weight = 15610.100| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 26289 Z= 0.228 Angle : 0.601 9.292 35880 Z= 0.309 Chirality : 0.046 0.192 4194 Planarity : 0.005 0.121 4533 Dihedral : 7.443 75.171 4626 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.94 % Favored : 94.67 % Rotamer: Outliers : 1.02 % Allowed : 7.89 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3117 helix: 1.30 (0.21), residues: 669 sheet: 0.68 (0.18), residues: 726 loop : -1.10 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.018 0.002 TYR A1067 PHE 0.017 0.002 PHE B 429 TRP 0.009 0.002 TRP B 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00553 (26187) covalent geometry : angle 0.58410 (35625) SS BOND : bond 0.00274 ( 42) SS BOND : angle 0.68727 ( 84) hydrogen bonds : bond 0.05813 ( 994) hydrogen bonds : angle 4.98325 ( 2829) Misc. bond : bond 0.00104 ( 3) link_BETA1-4 : bond 0.00300 ( 15) link_BETA1-4 : angle 1.22012 ( 45) link_NAG-ASN : bond 0.00292 ( 42) link_NAG-ASN : angle 2.34939 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.962 Fit side-chains REVERT: A 606 ASN cc_start: 0.8617 (t0) cc_final: 0.8321 (t0) REVERT: A 933 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8336 (tmtt) REVERT: B 569 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 1029 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8533 (ttp) outliers start: 28 outliers final: 18 residues processed: 125 average time/residue: 0.1231 time to fit residues: 27.8043 Evaluate side-chains 119 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105777 restraints weight = 46028.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109041 restraints weight = 27953.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109614 restraints weight = 18488.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110005 restraints weight = 16207.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110260 restraints weight = 15421.699| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26289 Z= 0.131 Angle : 0.529 9.310 35880 Z= 0.272 Chirality : 0.044 0.194 4194 Planarity : 0.005 0.120 4533 Dihedral : 7.039 73.413 4626 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.07 % Favored : 95.54 % Rotamer: Outliers : 0.98 % Allowed : 8.83 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3117 helix: 1.54 (0.21), residues: 669 sheet: 0.69 (0.18), residues: 726 loop : -1.04 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00304 (26187) covalent geometry : angle 0.51319 (35625) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.60076 ( 84) hydrogen bonds : bond 0.04870 ( 994) hydrogen bonds : angle 4.78300 ( 2829) Misc. bond : bond 0.00080 ( 3) link_BETA1-4 : bond 0.00385 ( 15) link_BETA1-4 : angle 1.12839 ( 45) link_NAG-ASN : bond 0.00257 ( 42) link_NAG-ASN : angle 2.14255 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.816 Fit side-chains REVERT: A 606 ASN cc_start: 0.8596 (t0) cc_final: 0.8302 (t0) REVERT: A 933 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8240 (tmtt) REVERT: B 126 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7743 (p) REVERT: B 569 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 1029 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8545 (ttp) REVERT: C 126 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (p) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 0.1296 time to fit residues: 29.5431 Evaluate side-chains 118 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 99 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 804 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100072 restraints weight = 46519.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102666 restraints weight = 30427.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102917 restraints weight = 22095.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103841 restraints weight = 19750.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104005 restraints weight = 18027.775| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 26289 Z= 0.313 Angle : 0.682 10.374 35880 Z= 0.351 Chirality : 0.049 0.189 4194 Planarity : 0.005 0.120 4533 Dihedral : 7.520 78.007 4626 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.68 % Favored : 93.94 % Rotamer: Outliers : 1.16 % Allowed : 9.38 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3117 helix: 0.99 (0.20), residues: 669 sheet: 0.43 (0.18), residues: 732 loop : -1.30 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.019 0.002 TYR A1067 PHE 0.021 0.002 PHE B 429 TRP 0.010 0.002 TRP B 436 HIS 0.007 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00760 (26187) covalent geometry : angle 0.66522 (35625) SS BOND : bond 0.00344 ( 42) SS BOND : angle 0.97156 ( 84) hydrogen bonds : bond 0.06466 ( 994) hydrogen bonds : angle 5.20283 ( 2829) Misc. bond : bond 0.00117 ( 3) link_BETA1-4 : bond 0.00239 ( 15) link_BETA1-4 : angle 1.31774 ( 45) link_NAG-ASN : bond 0.00353 ( 42) link_NAG-ASN : angle 2.46162 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.791 Fit side-chains REVERT: A 606 ASN cc_start: 0.8625 (t0) cc_final: 0.8352 (t0) REVERT: A 933 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8377 (tmtt) REVERT: B 569 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8400 (mp) REVERT: B 1029 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8594 (ttp) outliers start: 32 outliers final: 24 residues processed: 125 average time/residue: 0.1212 time to fit residues: 27.4750 Evaluate side-chains 126 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 901 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105622 restraints weight = 44544.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108213 restraints weight = 26041.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108642 restraints weight = 17993.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109086 restraints weight = 17000.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109261 restraints weight = 16089.496| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26289 Z= 0.109 Angle : 0.536 11.301 35880 Z= 0.275 Chirality : 0.044 0.193 4194 Planarity : 0.005 0.118 4533 Dihedral : 6.875 74.634 4626 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.95 % Favored : 95.67 % Rotamer: Outliers : 1.02 % Allowed : 9.81 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3117 helix: 1.58 (0.21), residues: 666 sheet: 0.54 (0.18), residues: 738 loop : -1.10 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00241 (26187) covalent geometry : angle 0.51990 (35625) SS BOND : bond 0.00185 ( 42) SS BOND : angle 0.71215 ( 84) hydrogen bonds : bond 0.04794 ( 994) hydrogen bonds : angle 4.82650 ( 2829) Misc. bond : bond 0.00075 ( 3) link_BETA1-4 : bond 0.00492 ( 15) link_BETA1-4 : angle 1.19604 ( 45) link_NAG-ASN : bond 0.00290 ( 42) link_NAG-ASN : angle 2.13325 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.950 Fit side-chains REVERT: A 606 ASN cc_start: 0.8524 (t0) cc_final: 0.8258 (t0) REVERT: A 938 LEU cc_start: 0.7482 (mt) cc_final: 0.7178 (mt) REVERT: B 126 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7729 (p) REVERT: B 569 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 878 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8809 (mt) REVERT: B 1029 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8518 (ttp) REVERT: C 126 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (p) REVERT: C 878 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8757 (mt) outliers start: 28 outliers final: 17 residues processed: 135 average time/residue: 0.1324 time to fit residues: 32.1702 Evaluate side-chains 127 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 46 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102931 restraints weight = 46318.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105165 restraints weight = 30782.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105679 restraints weight = 22146.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106278 restraints weight = 18655.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106618 restraints weight = 17285.557| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26289 Z= 0.174 Angle : 0.569 10.637 35880 Z= 0.291 Chirality : 0.045 0.190 4194 Planarity : 0.005 0.118 4533 Dihedral : 6.897 75.356 4626 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.26 % Favored : 94.35 % Rotamer: Outliers : 0.98 % Allowed : 9.85 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3117 helix: 1.47 (0.21), residues: 666 sheet: 0.52 (0.18), residues: 735 loop : -1.10 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.013 0.001 PHE B1121 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00420 (26187) covalent geometry : angle 0.55250 (35625) SS BOND : bond 0.00210 ( 42) SS BOND : angle 0.75336 ( 84) hydrogen bonds : bond 0.05263 ( 994) hydrogen bonds : angle 4.88887 ( 2829) Misc. bond : bond 0.00080 ( 3) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.22249 ( 45) link_NAG-ASN : bond 0.00242 ( 42) link_NAG-ASN : angle 2.22090 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.940 Fit side-chains REVERT: A 68 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5736 (mp) REVERT: B 126 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 569 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 933 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8181 (mmpt) REVERT: B 1029 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8487 (ttp) REVERT: C 126 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8291 (p) outliers start: 27 outliers final: 20 residues processed: 126 average time/residue: 0.1212 time to fit residues: 27.8227 Evaluate side-chains 127 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 64 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.131309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105791 restraints weight = 45904.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108279 restraints weight = 30129.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108556 restraints weight = 22034.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109940 restraints weight = 18267.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109957 restraints weight = 15682.677| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26289 Z= 0.127 Angle : 0.536 10.672 35880 Z= 0.275 Chirality : 0.044 0.189 4194 Planarity : 0.005 0.118 4533 Dihedral : 6.647 73.822 4626 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.14 % Favored : 95.48 % Rotamer: Outliers : 0.91 % Allowed : 10.11 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3117 helix: 1.67 (0.21), residues: 666 sheet: 0.60 (0.18), residues: 729 loop : -1.03 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00297 (26187) covalent geometry : angle 0.52058 (35625) SS BOND : bond 0.00184 ( 42) SS BOND : angle 0.68169 ( 84) hydrogen bonds : bond 0.04717 ( 994) hydrogen bonds : angle 4.76073 ( 2829) Misc. bond : bond 0.00068 ( 3) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.14753 ( 45) link_NAG-ASN : bond 0.00251 ( 42) link_NAG-ASN : angle 2.10544 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.972 Fit side-chains REVERT: A 606 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7755 (m110) REVERT: A 938 LEU cc_start: 0.7447 (mt) cc_final: 0.7122 (mt) REVERT: B 569 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 933 LYS cc_start: 0.8376 (mmtp) cc_final: 0.8153 (mmpt) REVERT: B 1029 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8522 (ttp) REVERT: C 126 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (p) outliers start: 25 outliers final: 19 residues processed: 128 average time/residue: 0.1256 time to fit residues: 29.2915 Evaluate side-chains 129 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 305 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 240 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.130926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105246 restraints weight = 45780.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108121 restraints weight = 29674.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108851 restraints weight = 20462.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109227 restraints weight = 16588.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109459 restraints weight = 15632.133| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26289 Z= 0.111 Angle : 0.527 10.639 35880 Z= 0.270 Chirality : 0.044 0.187 4194 Planarity : 0.005 0.117 4533 Dihedral : 6.575 73.005 4626 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.40 % Favored : 95.22 % Rotamer: Outliers : 0.91 % Allowed : 10.40 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3117 helix: 1.90 (0.21), residues: 648 sheet: 0.57 (0.18), residues: 738 loop : -0.97 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE A1121 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00255 (26187) covalent geometry : angle 0.51195 (35625) SS BOND : bond 0.00177 ( 42) SS BOND : angle 0.60138 ( 84) hydrogen bonds : bond 0.04577 ( 994) hydrogen bonds : angle 4.72098 ( 2829) Misc. bond : bond 0.00063 ( 3) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.14992 ( 45) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 2.08998 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.96 seconds wall clock time: 50 minutes 19.58 seconds (3019.58 seconds total)