Starting phenix.real_space_refine on Sun Jul 5 05:59:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgx_32491/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgx_32491/07_2026/7wgx_32491.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 9 Time building chain proxies: 4.90, per 1000 atoms: 0.19 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: 2.84 Conformation dependent library (CDL) restraints added in 794.2 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: 1.00 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: 6.22 Time building geometry restraints manager: 2.86 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: 13931 17.97 - 35.94: 940 35.94 - 53.91: 174 53.91 - 71.89: 33 71.89 - 89.86: 39 Dihedral angle restraints: 15117 sinusoidal: 5910 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 15114 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: 0.07 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: 1.300 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.480 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 13.431 89.857 9063 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/Z covalent geometry : bond 0.01743 / 0.87 (26187) covalent geometry : angle 1.19728 / 0.45 (35625) SS BOND : bond 0.00198 / 0.13 ( 42) SS BOND : angle 0.97612 / 0.60 ( 84) hydrogen bonds : bond 0.11537 / 7.55 ( 994) hydrogen bonds : angle 6.07389 / 4.29 ( 2829) Misc. bond : bond 0.09463 / 4.74 ( 3) link_BETA1-4 : bond 0.00332 / 0.20 ( 15) link_BETA1-4 : angle 0.52161 / 0.35 ( 45) link_NAG-ASN : bond 0.00390 / 0.24 ( 42) link_NAG-ASN : angle 2.40249 / 1.74 ( 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 : 0.983 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: 0.1575 time to fit residues: 43.8074 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 : 1.020 ------------------------------------------------------------------------------- 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... 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 = 0.3914 r_free = 0.3914 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108783 restraints weight = 46067.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110598 restraints weight = 31290.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112045 restraints weight = 22281.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113683 restraints weight = 19369.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113943 restraints weight = 17102.173| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26289 Z= 0.231 Angle : 0.650 9.748 35880 Z= 0.328 Chirality : 0.048 0.220 4194 Planarity : 0.005 0.119 4533 Dihedral : 6.873 81.693 3429 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.65 % Favored : 94.96 % Rotamer: Outliers : 0.40 % Allowed : 3.60 % Favored : 96.00 % 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: 1.17 (0.21), residues: 666 sheet: 0.80 (0.18), residues: 726 loop : -1.08 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.023 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/Z covalent geometry : bond 0.00559 / 0.23 (26187) covalent geometry : angle 0.63293 / 0.32 (35625) SS BOND : bond 0.00270 / 0.18 ( 42) SS BOND : angle 0.75065 / 0.49 ( 84) hydrogen bonds : bond 0.05900 / 3.80 ( 994) hydrogen bonds : angle 5.08586 / 3.58 ( 2829) Misc. bond : bond 0.00021 / 0.01 ( 3) link_BETA1-4 : bond 0.00502 / 0.29 ( 15) link_BETA1-4 : angle 0.96942 / 0.69 ( 45) link_NAG-ASN : bond 0.00395 / 0.25 ( 42) link_NAG-ASN : angle 2.54801 / 1.75 ( 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 : 0.922 Fit side-chains REVERT: A 606 ASN cc_start: 0.8444 (t0) cc_final: 0.8126 (t0) REVERT: C 427 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7666 (t0) REVERT: C 697 MET cc_start: 0.8331 (ptm) cc_final: 0.8108 (ptp) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.1345 time to fit residues: 28.4334 Evaluate side-chains 107 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 0.4980 chunk 72 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 935 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.107962 restraints weight = 46292.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110296 restraints weight = 30069.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111009 restraints weight = 21434.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111429 restraints weight = 17786.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111729 restraints weight = 16776.360| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26289 Z= 0.133 Angle : 0.535 8.349 35880 Z= 0.275 Chirality : 0.044 0.193 4194 Planarity : 0.005 0.119 4533 Dihedral : 6.386 76.315 3429 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.04 % Favored : 95.57 % Rotamer: Outliers : 0.44 % Allowed : 5.02 % Favored : 94.55 % 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: -0.03 (0.15), residues: 3117 helix: 1.46 (0.21), residues: 666 sheet: 0.82 (0.18), residues: 726 loop : -1.03 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE B1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (26187) covalent geometry : angle 0.51743 / 0.27 (35625) SS BOND : bond 0.00201 / 0.15 ( 42) SS BOND : angle 0.60321 / 0.40 ( 84) hydrogen bonds : bond 0.05005 / 3.23 ( 994) hydrogen bonds : angle 4.85064 / 3.42 ( 2829) Misc. bond : bond 0.00142 / 0.07 ( 3) link_BETA1-4 : bond 0.00394 / 0.23 ( 15) link_BETA1-4 : angle 1.02441 / 0.73 ( 45) link_NAG-ASN : bond 0.00306 / 0.19 ( 42) link_NAG-ASN : angle 2.28096 / 1.55 ( 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 123 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.030 Fit side-chains REVERT: A 606 ASN cc_start: 0.8455 (t0) cc_final: 0.8104 (t0) REVERT: B 569 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8164 (mp) outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 0.1216 time to fit residues: 26.3288 Evaluate side-chains 112 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP 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 C residue 571 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 271 optimal weight: 0.6980 chunk 280 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.108490 restraints weight = 46169.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110586 restraints weight = 28301.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111030 restraints weight = 21108.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111640 restraints weight = 18277.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111947 restraints weight = 17092.188| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 26289 Z= 0.100 Angle : 0.502 10.684 35880 Z= 0.257 Chirality : 0.043 0.187 4194 Planarity : 0.005 0.119 4533 Dihedral : 6.000 72.561 3429 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.40 % Favored : 95.22 % Rotamer: Outliers : 0.36 % Allowed : 6.76 % Favored : 92.88 % 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: 1.86 (0.21), residues: 651 sheet: 0.72 (0.17), residues: 786 loop : -0.89 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.017 0.001 TYR A1067 PHE 0.013 0.001 PHE A 65 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26187) covalent geometry : angle 0.48693 / 0.25 (35625) SS BOND : bond 0.00151 / 0.11 ( 42) SS BOND : angle 0.53889 / 0.36 ( 84) hydrogen bonds : bond 0.04238 / 2.74 ( 994) hydrogen bonds : angle 4.63833 / 3.27 ( 2829) Misc. bond : bond 0.00079 / 0.04 ( 3) link_BETA1-4 : bond 0.00378 / 0.23 ( 15) link_BETA1-4 : angle 0.99909 / 0.71 ( 45) link_NAG-ASN : bond 0.00289 / 0.19 ( 42) link_NAG-ASN : angle 2.06488 / 1.40 ( 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 126 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.938 Fit side-chains REVERT: A 606 ASN cc_start: 0.8544 (t0) cc_final: 0.7886 (m-40) REVERT: A 933 LYS cc_start: 0.8526 (mmtp) cc_final: 0.8264 (tmtt) REVERT: A 938 LEU cc_start: 0.7562 (mt) cc_final: 0.7341 (mt) REVERT: B 153 MET cc_start: 0.7823 (mmm) cc_final: 0.7588 (mmm) REVERT: B 569 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8130 (mp) outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 0.1296 time to fit residues: 28.3239 Evaluate side-chains 114 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 299 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 295 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 227 optimal weight: 0.0980 chunk 177 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 901 GLN B 955 ASN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108099 restraints weight = 44495.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111826 restraints weight = 24083.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114236 restraints weight = 16336.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115749 restraints weight = 12709.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116721 restraints weight = 10799.595| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26289 Z= 0.094 Angle : 0.485 9.563 35880 Z= 0.249 Chirality : 0.043 0.179 4194 Planarity : 0.005 0.119 4533 Dihedral : 5.641 68.359 3429 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.11 % Favored : 95.51 % Rotamer: Outliers : 0.87 % Allowed : 6.83 % Favored : 92.29 % 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: 0.31 (0.15), residues: 3117 helix: 2.10 (0.21), residues: 651 sheet: 0.67 (0.17), residues: 792 loop : -0.82 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE B 65 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (26187) covalent geometry : angle 0.47029 / 0.25 (35625) SS BOND : bond 0.00135 / 0.09 ( 42) SS BOND : angle 0.51177 / 0.34 ( 84) hydrogen bonds : bond 0.03962 / 2.56 ( 994) hydrogen bonds : angle 4.50869 / 3.18 ( 2829) Misc. bond : bond 0.00052 / 0.03 ( 3) link_BETA1-4 : bond 0.00391 / 0.24 ( 15) link_BETA1-4 : angle 0.99816 / 0.70 ( 45) link_NAG-ASN : bond 0.00290 / 0.18 ( 42) link_NAG-ASN : angle 1.97543 / 1.33 ( 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 138 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.065 Fit side-chains REVERT: A 606 ASN cc_start: 0.8557 (t0) cc_final: 0.8237 (t0) REVERT: B 153 MET cc_start: 0.7578 (mmm) cc_final: 0.7310 (mmm) REVERT: B 569 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8136 (mp) outliers start: 24 outliers final: 6 residues processed: 134 average time/residue: 0.1339 time to fit residues: 32.3444 Evaluate side-chains 111 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 50 optimal weight: 0.0040 chunk 98 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 244 optimal weight: 0.0770 overall best weight: 1.7754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106997 restraints weight = 46165.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108680 restraints weight = 31699.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109310 restraints weight = 23164.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109866 restraints weight = 19931.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110197 restraints weight = 18467.276| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26289 Z= 0.148 Angle : 0.531 9.268 35880 Z= 0.273 Chirality : 0.044 0.177 4194 Planarity : 0.005 0.122 4533 Dihedral : 5.704 68.988 3429 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.78 % Favored : 94.83 % Rotamer: Outliers : 1.02 % Allowed : 7.42 % Favored : 91.57 % 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: 1.88 (0.21), residues: 651 sheet: 0.74 (0.18), residues: 738 loop : -0.86 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE A 65 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (26187) covalent geometry : angle 0.51631 / 0.27 (35625) SS BOND : bond 0.00193 / 0.13 ( 42) SS BOND : angle 0.54588 / 0.37 ( 84) hydrogen bonds : bond 0.04844 / 3.13 ( 994) hydrogen bonds : angle 4.67724 / 3.29 ( 2829) Misc. bond : bond 0.00060 / 0.03 ( 3) link_BETA1-4 : bond 0.00308 / 0.18 ( 15) link_BETA1-4 : angle 1.07655 / 0.76 ( 45) link_NAG-ASN : bond 0.00243 / 0.16 ( 42) link_NAG-ASN : angle 2.07313 / 1.39 ( 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 138 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.870 Fit side-chains REVERT: A 606 ASN cc_start: 0.8602 (t0) cc_final: 0.8351 (t0) REVERT: B 126 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7700 (p) REVERT: B 153 MET cc_start: 0.7609 (mmm) cc_final: 0.7344 (mmm) REVERT: B 569 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 1029 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8461 (ttp) REVERT: C 126 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8246 (p) REVERT: C 318 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6019 (t80) outliers start: 28 outliers final: 15 residues processed: 129 average time/residue: 0.1269 time to fit residues: 29.7893 Evaluate side-chains 122 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 126 VAL 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 1029 MET 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 318 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 849 LEU 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: 4.9990 chunk 56 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 257 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN B 960 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106748 restraints weight = 46279.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108359 restraints weight = 30501.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109088 restraints weight = 22728.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109579 restraints weight = 19253.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109917 restraints weight = 17821.010| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1986 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= 0.141 Angle : 0.522 9.048 35880 Z= 0.269 Chirality : 0.044 0.175 4194 Planarity : 0.005 0.120 4533 Dihedral : 5.673 68.832 3429 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.20 % Favored : 95.41 % Rotamer: Outliers : 0.80 % Allowed : 8.36 % Favored : 90.84 % 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: 0.17 (0.15), residues: 3117 helix: 1.91 (0.21), residues: 648 sheet: 0.69 (0.18), residues: 738 loop : -0.88 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.012 0.001 PHE B1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (26187) covalent geometry : angle 0.50763 / 0.27 (35625) SS BOND : bond 0.00185 / 0.13 ( 42) SS BOND : angle 0.58461 / 0.40 ( 84) hydrogen bonds : bond 0.04751 / 3.06 ( 994) hydrogen bonds : angle 4.67808 / 3.29 ( 2829) Misc. bond : bond 0.00056 / 0.03 ( 3) link_BETA1-4 : bond 0.00341 / 0.21 ( 15) link_BETA1-4 : angle 1.07624 / 0.77 ( 45) link_NAG-ASN : bond 0.00239 / 0.15 ( 42) link_NAG-ASN : angle 2.04335 / 1.37 ( 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 127 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.038 Fit side-chains REVERT: A 606 ASN cc_start: 0.8555 (t0) cc_final: 0.8327 (t0) REVERT: B 126 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7731 (p) REVERT: B 153 MET cc_start: 0.7560 (mmm) cc_final: 0.7248 (mmm) REVERT: B 569 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 1029 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8487 (ttp) REVERT: C 126 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8263 (p) REVERT: C 318 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6337 (t80) outliers start: 22 outliers final: 13 residues processed: 120 average time/residue: 0.1357 time to fit residues: 29.3713 Evaluate side-chains 119 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 126 VAL 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 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 849 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108462 restraints weight = 45986.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110840 restraints weight = 29506.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111523 restraints weight = 20279.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112016 restraints weight = 17606.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112294 restraints weight = 16510.763| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2015 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= 0.104 Angle : 0.499 9.002 35880 Z= 0.257 Chirality : 0.043 0.174 4194 Planarity : 0.005 0.118 4533 Dihedral : 5.489 66.666 3429 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.40 % Favored : 95.22 % Rotamer: Outliers : 0.84 % Allowed : 8.65 % Favored : 90.51 % 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: 0.29 (0.15), residues: 3117 helix: 2.11 (0.21), residues: 648 sheet: 0.72 (0.18), residues: 738 loop : -0.82 (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 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (26187) covalent geometry : angle 0.48464 / 0.25 (35625) SS BOND : bond 0.00146 / 0.10 ( 42) SS BOND : angle 0.52573 / 0.36 ( 84) hydrogen bonds : bond 0.04221 / 2.73 ( 994) hydrogen bonds : angle 4.54706 / 3.20 ( 2829) Misc. bond : bond 0.00048 / 0.02 ( 3) link_BETA1-4 : bond 0.00399 / 0.24 ( 15) link_BETA1-4 : angle 1.05594 / 0.75 ( 45) link_NAG-ASN : bond 0.00256 / 0.16 ( 42) link_NAG-ASN : angle 1.94356 / 1.31 ( 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 138 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.046 Fit side-chains REVERT: A 606 ASN cc_start: 0.8498 (t0) cc_final: 0.8292 (t0) REVERT: B 126 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 153 MET cc_start: 0.7572 (mmm) cc_final: 0.7251 (mmm) REVERT: B 569 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 1029 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8446 (ttp) REVERT: C 126 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 318 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.6181 (t80) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 0.1213 time to fit residues: 29.6048 Evaluate side-chains 126 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 931 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 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 126 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 259 optimal weight: 0.0770 chunk 150 optimal weight: 0.3980 chunk 265 optimal weight: 4.9990 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105835 restraints weight = 46413.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107629 restraints weight = 33784.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108435 restraints weight = 23622.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109008 restraints weight = 19674.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109323 restraints weight = 18133.288| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26289 Z= 0.170 Angle : 0.549 11.020 35880 Z= 0.282 Chirality : 0.045 0.175 4194 Planarity : 0.005 0.118 4533 Dihedral : 5.636 68.020 3429 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.56 % Favored : 95.06 % Rotamer: Outliers : 0.95 % Allowed : 8.54 % Favored : 90.51 % 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: 0.09 (0.15), residues: 3117 helix: 1.77 (0.21), residues: 666 sheet: 0.64 (0.18), residues: 738 loop : -0.92 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE B 65 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (26187) covalent geometry : angle 0.53351 / 0.28 (35625) SS BOND : bond 0.00201 / 0.13 ( 42) SS BOND : angle 1.05323 / 0.77 ( 84) hydrogen bonds : bond 0.04995 / 3.22 ( 994) hydrogen bonds : angle 4.75239 / 3.33 ( 2829) Misc. bond : bond 0.00061 / 0.03 ( 3) link_BETA1-4 : bond 0.00324 / 0.19 ( 15) link_BETA1-4 : angle 1.12230 / 0.80 ( 45) link_NAG-ASN : bond 0.00236 / 0.15 ( 42) link_NAG-ASN : angle 2.06119 / 1.38 ( 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 130 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.839 Fit side-chains REVERT: A 606 ASN cc_start: 0.8525 (t0) cc_final: 0.8279 (t0) REVERT: B 126 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 153 MET cc_start: 0.7616 (mmm) cc_final: 0.7292 (mmm) REVERT: B 569 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 933 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8132 (mmpt) REVERT: B 1029 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: C 126 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 318 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6528 (t80) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 0.1375 time to fit residues: 29.9683 Evaluate side-chains 124 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL 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 931 ILE Chi-restraints excluded: chain B residue 1029 MET 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 318 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 64 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 306 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.133116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107673 restraints weight = 46007.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110453 restraints weight = 29898.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111222 restraints weight = 20639.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111622 restraints weight = 16730.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111850 restraints weight = 15747.719| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2139 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= 0.096 Angle : 0.499 10.965 35880 Z= 0.257 Chirality : 0.043 0.171 4194 Planarity : 0.005 0.117 4533 Dihedral : 5.424 65.543 3429 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.11 % Favored : 95.51 % Rotamer: Outliers : 0.65 % Allowed : 9.23 % Favored : 90.11 % 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: 0.30 (0.15), residues: 3117 helix: 2.16 (0.22), residues: 648 sheet: 0.69 (0.18), residues: 738 loop : -0.81 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.016 0.001 TYR C1067 PHE 0.019 0.001 PHE B 65 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (26187) covalent geometry : angle 0.48552 / 0.25 (35625) SS BOND : bond 0.00156 / 0.10 ( 42) SS BOND : angle 0.64809 / 0.46 ( 84) hydrogen bonds : bond 0.04097 / 2.65 ( 994) hydrogen bonds : angle 4.56113 / 3.20 ( 2829) Misc. bond : bond 0.00043 / 0.02 ( 3) link_BETA1-4 : bond 0.00383 / 0.23 ( 15) link_BETA1-4 : angle 1.04886 / 0.75 ( 45) link_NAG-ASN : bond 0.00272 / 0.17 ( 42) link_NAG-ASN : angle 1.90472 / 1.29 ( 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 128 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.837 Fit side-chains REVERT: A 606 ASN cc_start: 0.8401 (t0) cc_final: 0.8178 (t0) REVERT: B 126 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7690 (p) REVERT: B 153 MET cc_start: 0.7624 (mmm) cc_final: 0.7254 (mmm) REVERT: B 569 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 933 LYS cc_start: 0.8370 (mmtp) cc_final: 0.8135 (mmpt) REVERT: B 1029 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8437 (ttp) REVERT: C 126 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 318 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.6204 (t80) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.1230 time to fit residues: 27.5707 Evaluate side-chains 123 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 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 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 931 ILE 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 318 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 305 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103047 restraints weight = 45197.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104944 restraints weight = 29436.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105993 restraints weight = 21247.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108061 restraints weight = 18904.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108299 restraints weight = 15652.890| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26289 Z= 0.255 Angle : 0.630 11.203 35880 Z= 0.324 Chirality : 0.047 0.173 4194 Planarity : 0.005 0.117 4533 Dihedral : 5.907 71.301 3429 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.49 % Favored : 94.13 % Rotamer: Outliers : 0.69 % Allowed : 9.31 % Favored : 90.00 % 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: -0.13 (0.15), residues: 3117 helix: 1.45 (0.21), residues: 666 sheet: 0.58 (0.18), residues: 729 loop : -1.04 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1107 TYR 0.020 0.002 TYR C1067 PHE 0.019 0.002 PHE C 86 TRP 0.010 0.002 TRP B 436 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (26187) covalent geometry : angle 0.61478 / 0.32 (35625) SS BOND : bond 0.00320 / 0.20 ( 42) SS BOND : angle 0.83812 / 0.57 ( 84) hydrogen bonds : bond 0.06010 / 3.86 ( 994) hydrogen bonds : angle 5.01905 / 3.51 ( 2829) Misc. bond : bond 0.00065 / 0.03 ( 3) link_BETA1-4 : bond 0.00299 / 0.19 ( 15) link_BETA1-4 : angle 1.25203 / 0.88 ( 45) link_NAG-ASN : bond 0.00283 / 0.18 ( 42) link_NAG-ASN : angle 2.26259 / 1.51 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.54 seconds wall clock time: 54 minutes 20.34 seconds (3260.34 seconds total)