Starting phenix.real_space_refine on Fri Mar 6 05:32:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kj2_22891/03_2026/7kj2_22891.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 130 5.16 5 C 18187 2.51 5 N 4643 2.21 5 O 5600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28560 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7566 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 918} Chain breaks: 11 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7661 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7509 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 48, 'TRANS': 912} Chain breaks: 10 Chain: "D" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.07, per 1000 atoms: 0.25 Number of scatterers: 28560 At special positions: 0 Unit cell: (133.65, 160.875, 233.475, 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 130 16.00 O 5600 8.00 N 4643 7.00 C 18187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.09 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.42 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.49 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.49 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.85 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.88 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.61 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.38 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.32 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.10 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 Atom "HETATM28390 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM28306 O5 NAG B1308 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN D 53 " " NAG R 1 " - " ASN D 90 " " NAG S 1 " - " ASN D 103 " " NAG T 1 " - " ASN D 432 " " NAG U 1 " - " ASN D 546 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 34.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.624A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.200A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.736A 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 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.076A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.682A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.123A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.562A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.540A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.600A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.573A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.593A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.611A 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 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.559A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.742A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.695A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.528A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.011A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 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: 4.409A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.521A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.554A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.526A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) 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: 3.704A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.266A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.622A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.477A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 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: 3.640A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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: 3.636A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.881A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.571A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.743A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.555A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.278A 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: 3.720A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.716A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.460A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 3.881A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.538A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.843A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.689A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.509A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.013A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.707A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.713A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.699A pdb=" N TYR D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.389A pdb=" N ALA D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.647A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.054A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.723A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 465 " --> pdb=" O TRP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.536A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.239A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.559A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.288A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.707A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.447A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.533A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.646A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.342A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.645A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.599A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.770A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.600A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.718A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.169A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.041A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.694A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.331A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.958A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.704A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.558A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 584 through 585 removed outlier: 3.575A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.045A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.069A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.083A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.762A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.679A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.866A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.903A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.691A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.407A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.374A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.374A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.516A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.164A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 350 1245 hydrogen bonds defined for protein. 3438 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: 7.34 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4777 1.30 - 1.44: 7912 1.44 - 1.58: 16316 1.58 - 1.72: 17 1.72 - 1.86: 175 Bond restraints: 29197 Sorted by residual: bond pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " ideal model delta sigma weight residual 1.524 1.640 -0.115 1.22e-02 6.72e+03 8.90e+01 bond pdb=" CA CYS B 480 " pdb=" C CYS B 480 " ideal model delta sigma weight residual 1.519 1.602 -0.083 1.14e-02 7.69e+03 5.26e+01 bond pdb=" N CYS A 749 " pdb=" CA CYS A 749 " ideal model delta sigma weight residual 1.459 1.389 0.070 1.17e-02 7.31e+03 3.55e+01 bond pdb=" N CYS B 480 " pdb=" CA CYS B 480 " ideal model delta sigma weight residual 1.461 1.525 -0.064 1.20e-02 6.94e+03 2.80e+01 bond pdb=" CG ASN A 61 " pdb=" ND2 ASN A 61 " ideal model delta sigma weight residual 1.328 1.429 -0.101 2.10e-02 2.27e+03 2.30e+01 ... (remaining 29192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 34373 2.70 - 5.40: 5063 5.40 - 8.10: 236 8.10 - 10.80: 25 10.80 - 13.50: 6 Bond angle restraints: 39703 Sorted by residual: angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 111.28 122.66 -11.38 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N CYS C 131 " pdb=" CA CYS C 131 " pdb=" C CYS C 131 " ideal model delta sigma weight residual 110.35 123.85 -13.50 1.36e+00 5.41e-01 9.85e+01 angle pdb=" C ASN A 61 " pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 123.14 110.70 12.44 1.31e+00 5.83e-01 9.02e+01 angle pdb=" N CYS D 542 " pdb=" CA CYS D 542 " pdb=" C CYS D 542 " ideal model delta sigma weight residual 109.96 123.25 -13.29 1.49e+00 4.50e-01 7.95e+01 angle pdb=" N ARG B 983 " pdb=" CA ARG B 983 " pdb=" C ARG B 983 " ideal model delta sigma weight residual 113.28 123.06 -9.78 1.22e+00 6.72e-01 6.43e+01 ... (remaining 39698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 16807 18.31 - 36.62: 1135 36.62 - 54.93: 229 54.93 - 73.24: 76 73.24 - 91.54: 33 Dihedral angle restraints: 18280 sinusoidal: 8072 harmonic: 10208 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 178.12 -85.12 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.97 -84.97 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 9.22 83.78 1 1.00e+01 1.00e-02 8.56e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.630: 4650 0.630 - 1.259: 20 1.259 - 1.889: 5 1.889 - 2.519: 0 2.519 - 3.148: 1 Chirality restraints: 4676 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 0.75 -3.15 2.00e-01 2.50e+01 2.48e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.30e+01 ... (remaining 4673 not shown) Planarity restraints: 5087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG S 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 53 " 0.229 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" CG ASN D 53 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN D 53 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN D 53 " -0.420 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " -0.178 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" CG ASN B 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " 0.442 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.271 2.00e-02 2.50e+03 ... (remaining 5084 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 21 2.36 - 2.99: 14053 2.99 - 3.63: 39291 3.63 - 4.26: 66630 4.26 - 4.90: 109057 Nonbonded interactions: 229052 Sorted by model distance: nonbonded pdb=" OD1 ASN A 121 " pdb=" O ASN A 125 " model vdw 1.722 3.040 nonbonded pdb=" CD1 LEU D 351 " pdb=" NE ARG D 357 " model vdw 1.967 2.832 nonbonded pdb=" OE2 GLU B 773 " pdb=" NH1 ARG B1019 " model vdw 2.107 3.120 nonbonded pdb=" OD1 ASN C 331 " pdb=" N2 NAG C1305 " model vdw 2.148 3.120 nonbonded pdb=" OD1 ASN A 801 " pdb=" OG SER A 803 " model vdw 2.153 3.040 ... (remaining 229047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 442 \ or resid 450 through 451 or resid 453 or resid 455 or resid 457 through 458 or r \ esid 463 through 470 or resid 491 through 505 or (resid 506 and (name N or name \ CA or name C or name O or name CB )) or resid 507 through 515 or resid 522 throu \ gh 827 or resid 856 through 1310)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 241 or (resid 242 through 263 and (name N or name CA o \ r name C or name O or name CB )) or resid 265 through 442 or resid 450 through 4 \ 51 or resid 453 or resid 455 or resid 457 through 458 or resid 463 through 470 o \ r resid 491 through 501 or resid 503 through 676 or resid 690 through 827 or res \ id 856 through 1310)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 241 \ or (resid 242 through 264 and (name N or name CA or name C or name O or name CB \ )) or resid 265 through 442 or resid 448 through 449 or resid 451 through 452 or \ resid 454 through 501 or resid 503 through 505 or (resid 506 and (name N or nam \ e CA or name C or name O or name CB )) or resid 507 through 515 or resid 522 thr \ ough 1310)) } ncs_group { reference = 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 7.020 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.880 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.018 0.852 29308 Z= 0.980 Angle : 2.139 67.541 39993 Z= 1.278 Chirality : 0.141 3.148 4676 Planarity : 0.014 0.305 5034 Dihedral : 13.460 91.545 11572 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.38 % Favored : 93.12 % Rotamer: Outliers : 1.69 % Allowed : 3.38 % Favored : 94.93 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 3432 helix: -2.14 (0.13), residues: 993 sheet: -0.37 (0.20), residues: 539 loop : -1.40 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 393 TYR 0.110 0.021 TYR A 421 PHE 0.089 0.014 PHE B 898 TRP 0.213 0.032 TRP C 104 HIS 0.014 0.004 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01346 (29197) covalent geometry : angle 1.80989 (39703) SS BOND : bond 0.25101 ( 40) SS BOND : angle 10.64469 ( 80) hydrogen bonds : bond 0.18109 ( 1230) hydrogen bonds : angle 8.63630 ( 3438) Misc. bond : bond 0.16648 ( 1) link_BETA1-4 : bond 0.05466 ( 17) link_BETA1-4 : angle 3.51644 ( 51) link_NAG-ASN : bond 0.16601 ( 53) link_NAG-ASN : angle 16.50080 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 614 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1031 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8576 (mt-10) REVERT: B 886 TRP cc_start: 0.7987 (p90) cc_final: 0.7632 (p90) REVERT: B 931 ILE cc_start: 0.9105 (mm) cc_final: 0.8498 (mm) REVERT: C 129 LYS cc_start: 0.6696 (mttt) cc_final: 0.6334 (mttm) REVERT: C 305 SER cc_start: 0.8611 (t) cc_final: 0.8368 (p) REVERT: C 716 THR cc_start: 0.7530 (p) cc_final: 0.7233 (t) REVERT: D 429 GLN cc_start: 0.7124 (mm110) cc_final: 0.6551 (tm-30) REVERT: D 568 LEU cc_start: 0.6430 (tp) cc_final: 0.6135 (tp) outliers start: 52 outliers final: 15 residues processed: 655 average time/residue: 0.2102 time to fit residues: 212.4678 Evaluate side-chains 299 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 284 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain D residue 544 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 474 GLN B 690 GLN B 787 GLN B 907 ASN B 955 ASN B1048 HIS C 804 GLN C 907 ASN C 925 ASN C1048 HIS D 81 GLN D 149 ASN D 250 ASN D 330 ASN D 401 HIS D 472 GLN D 505 HIS D 599 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.159544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131313 restraints weight = 62565.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126388 restraints weight = 89021.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123357 restraints weight = 79283.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123493 restraints weight = 63580.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123707 restraints weight = 51532.093| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29308 Z= 0.161 Angle : 0.805 19.455 39993 Z= 0.397 Chirality : 0.051 0.516 4676 Planarity : 0.004 0.042 5034 Dihedral : 7.265 59.827 5227 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 2.28 % Allowed : 9.63 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3432 helix: 0.01 (0.15), residues: 1037 sheet: -0.25 (0.18), residues: 642 loop : -0.84 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1091 TYR 0.025 0.002 TYR A 265 PHE 0.028 0.002 PHE D 438 TRP 0.028 0.002 TRP B1102 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00351 (29197) covalent geometry : angle 0.73285 (39703) SS BOND : bond 0.00551 ( 40) SS BOND : angle 2.44498 ( 80) hydrogen bonds : bond 0.04890 ( 1230) hydrogen bonds : angle 6.06159 ( 3438) Misc. bond : bond 0.00299 ( 1) link_BETA1-4 : bond 0.00647 ( 17) link_BETA1-4 : angle 2.18883 ( 51) link_NAG-ASN : bond 0.00748 ( 53) link_NAG-ASN : angle 4.95121 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 367 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.4609 (t0) cc_final: 0.4207 (m110) REVERT: B 423 TYR cc_start: 0.5726 (t80) cc_final: 0.5488 (t80) REVERT: B 869 MET cc_start: 0.8297 (mtp) cc_final: 0.7629 (ttm) REVERT: B 1075 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6359 (p90) REVERT: B 1135 ASN cc_start: 0.7062 (t0) cc_final: 0.6800 (t0) REVERT: C 129 LYS cc_start: 0.7777 (mttt) cc_final: 0.7349 (mttm) REVERT: C 133 PHE cc_start: 0.5250 (m-80) cc_final: 0.4984 (t80) REVERT: C 305 SER cc_start: 0.8614 (t) cc_final: 0.8337 (p) REVERT: C 716 THR cc_start: 0.7897 (p) cc_final: 0.7644 (t) REVERT: C 1047 TYR cc_start: 0.8525 (m-80) cc_final: 0.8130 (m-80) REVERT: C 1139 ASP cc_start: 0.7643 (t0) cc_final: 0.7355 (t0) REVERT: D 401 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.5018 (t-90) REVERT: D 429 GLN cc_start: 0.6640 (mm110) cc_final: 0.6073 (pp30) REVERT: D 531 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.7004 (tt0) outliers start: 70 outliers final: 31 residues processed: 416 average time/residue: 0.1734 time to fit residues: 118.8508 Evaluate side-chains 295 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 187 optimal weight: 0.0070 chunk 103 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 289 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 314 GLN B 121 ASN B 164 ASN B 784 GLN B 955 ASN B1119 ASN C 81 ASN C 762 GLN C 907 ASN C 978 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 401 HIS D 442 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.154722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126233 restraints weight = 63702.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122445 restraints weight = 89626.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119731 restraints weight = 75055.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120248 restraints weight = 63330.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119587 restraints weight = 51824.386| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 29308 Z= 0.157 Angle : 0.711 18.621 39993 Z= 0.348 Chirality : 0.048 0.435 4676 Planarity : 0.004 0.046 5034 Dihedral : 6.462 58.554 5210 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.60 % Allowed : 10.67 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3432 helix: 0.57 (0.16), residues: 1028 sheet: -0.17 (0.18), residues: 646 loop : -0.75 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.028 0.002 TYR C 904 PHE 0.017 0.002 PHE D 438 TRP 0.020 0.002 TRP B1102 HIS 0.018 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00357 (29197) covalent geometry : angle 0.64798 (39703) SS BOND : bond 0.00399 ( 40) SS BOND : angle 2.08547 ( 80) hydrogen bonds : bond 0.04361 ( 1230) hydrogen bonds : angle 5.68072 ( 3438) Misc. bond : bond 0.00214 ( 1) link_BETA1-4 : bond 0.00536 ( 17) link_BETA1-4 : angle 2.07083 ( 51) link_NAG-ASN : bond 0.00812 ( 53) link_NAG-ASN : angle 4.30990 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.4278 (t0) cc_final: 0.4005 (m110) REVERT: B 869 MET cc_start: 0.8420 (mtp) cc_final: 0.8166 (ttm) REVERT: B 957 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 1075 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6288 (p90) REVERT: B 1135 ASN cc_start: 0.7354 (t0) cc_final: 0.7115 (t0) REVERT: C 129 LYS cc_start: 0.7557 (mttt) cc_final: 0.7203 (mttm) REVERT: C 305 SER cc_start: 0.8620 (t) cc_final: 0.8367 (p) REVERT: C 1047 TYR cc_start: 0.8597 (m-80) cc_final: 0.8199 (m-80) REVERT: D 429 GLN cc_start: 0.6370 (mm110) cc_final: 0.6033 (pp30) REVERT: D 474 MET cc_start: 0.5421 (mmm) cc_final: 0.5197 (mmm) outliers start: 80 outliers final: 59 residues processed: 342 average time/residue: 0.1701 time to fit residues: 96.6546 Evaluate side-chains 309 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 348 optimal weight: 20.0000 chunk 285 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 271 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN B1135 ASN C 81 ASN C 978 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 373 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.153753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124124 restraints weight = 62991.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118692 restraints weight = 90843.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.116202 restraints weight = 76851.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116508 restraints weight = 63093.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116545 restraints weight = 51431.809| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 29308 Z= 0.209 Angle : 0.712 18.743 39993 Z= 0.349 Chirality : 0.048 0.404 4676 Planarity : 0.004 0.049 5034 Dihedral : 6.313 59.473 5210 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 3.25 % Allowed : 11.48 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3432 helix: 0.86 (0.16), residues: 1011 sheet: -0.22 (0.18), residues: 660 loop : -0.73 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.030 0.002 TYR A 904 PHE 0.023 0.002 PHE D 504 TRP 0.021 0.002 TRP D 566 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00485 (29197) covalent geometry : angle 0.65215 (39703) SS BOND : bond 0.00715 ( 40) SS BOND : angle 2.08428 ( 80) hydrogen bonds : bond 0.04263 ( 1230) hydrogen bonds : angle 5.59496 ( 3438) Misc. bond : bond 0.00030 ( 1) link_BETA1-4 : bond 0.00564 ( 17) link_BETA1-4 : angle 1.94873 ( 51) link_NAG-ASN : bond 0.00754 ( 53) link_NAG-ASN : angle 4.21286 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 270 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8426 (mtp) cc_final: 0.7945 (ttm) REVERT: B 1075 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6465 (p90) REVERT: B 1096 VAL cc_start: 0.9135 (m) cc_final: 0.8902 (m) REVERT: B 1135 ASN cc_start: 0.7598 (t0) cc_final: 0.7248 (t0) REVERT: C 305 SER cc_start: 0.8652 (t) cc_final: 0.8385 (p) REVERT: C 1135 ASN cc_start: 0.7579 (t0) cc_final: 0.7355 (t0) REVERT: D 282 THR cc_start: 0.2844 (p) cc_final: 0.2436 (p) REVERT: D 429 GLN cc_start: 0.6502 (mm110) cc_final: 0.6187 (pp30) REVERT: D 474 MET cc_start: 0.5631 (mmm) cc_final: 0.5400 (mmm) outliers start: 100 outliers final: 73 residues processed: 349 average time/residue: 0.1832 time to fit residues: 106.2925 Evaluate side-chains 307 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 233 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 114 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 222 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 187 optimal weight: 0.0980 chunk 288 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 954 GLN B1119 ASN C 81 ASN C 978 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.153027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123229 restraints weight = 62979.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117484 restraints weight = 94896.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115519 restraints weight = 83096.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115590 restraints weight = 70845.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115657 restraints weight = 60246.554| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 29308 Z= 0.214 Angle : 0.708 18.815 39993 Z= 0.348 Chirality : 0.048 0.531 4676 Planarity : 0.004 0.050 5034 Dihedral : 6.203 59.943 5208 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 3.38 % Allowed : 12.72 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3432 helix: 0.84 (0.16), residues: 1020 sheet: -0.27 (0.18), residues: 684 loop : -0.77 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.030 0.002 TYR B 904 PHE 0.019 0.002 PHE B 759 TRP 0.016 0.002 TRP D 302 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00503 (29197) covalent geometry : angle 0.65188 (39703) SS BOND : bond 0.00663 ( 40) SS BOND : angle 2.36375 ( 80) hydrogen bonds : bond 0.04181 ( 1230) hydrogen bonds : angle 5.62856 ( 3438) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00555 ( 17) link_BETA1-4 : angle 1.89484 ( 51) link_NAG-ASN : bond 0.00758 ( 53) link_NAG-ASN : angle 4.01573 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 248 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 THR cc_start: 0.8774 (m) cc_final: 0.8573 (p) REVERT: B 869 MET cc_start: 0.8493 (mtp) cc_final: 0.8272 (ttm) REVERT: B 1075 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6428 (p90) REVERT: B 1096 VAL cc_start: 0.9139 (m) cc_final: 0.8887 (m) REVERT: B 1135 ASN cc_start: 0.7736 (t0) cc_final: 0.7422 (t0) REVERT: C 305 SER cc_start: 0.8667 (t) cc_final: 0.8406 (p) REVERT: D 429 GLN cc_start: 0.6620 (mm110) cc_final: 0.6280 (pp30) outliers start: 104 outliers final: 79 residues processed: 330 average time/residue: 0.1708 time to fit residues: 93.9914 Evaluate side-chains 310 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 329 optimal weight: 0.1980 chunk 219 optimal weight: 20.0000 chunk 193 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 261 optimal weight: 0.0370 chunk 322 optimal weight: 5.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 978 ASN ** D 149 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 = 0.4199 r_free = 0.4199 target = 0.154447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129802 restraints weight = 63181.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125580 restraints weight = 91076.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.123248 restraints weight = 90997.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123399 restraints weight = 89497.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.122460 restraints weight = 72117.710| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29308 Z= 0.140 Angle : 0.673 21.303 39993 Z= 0.324 Chirality : 0.048 0.802 4676 Planarity : 0.004 0.051 5034 Dihedral : 6.011 59.939 5208 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 2.76 % Allowed : 13.79 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3432 helix: 1.11 (0.16), residues: 1012 sheet: -0.06 (0.19), residues: 633 loop : -0.72 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.032 0.001 TYR B 904 PHE 0.017 0.001 PHE A 400 TRP 0.027 0.001 TRP B1102 HIS 0.026 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00319 (29197) covalent geometry : angle 0.60641 (39703) SS BOND : bond 0.00384 ( 40) SS BOND : angle 2.33535 ( 80) hydrogen bonds : bond 0.03768 ( 1230) hydrogen bonds : angle 5.46366 ( 3438) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00535 ( 17) link_BETA1-4 : angle 1.83321 ( 51) link_NAG-ASN : bond 0.00907 ( 53) link_NAG-ASN : angle 4.29248 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 252 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.5442 (mptt) cc_final: 0.3982 (mptt) REVERT: A 238 PHE cc_start: 0.4681 (p90) cc_final: 0.4434 (p90) REVERT: B 1075 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6282 (p90) REVERT: B 1096 VAL cc_start: 0.8994 (m) cc_final: 0.8749 (m) REVERT: B 1135 ASN cc_start: 0.7585 (t0) cc_final: 0.7314 (t0) REVERT: C 305 SER cc_start: 0.8575 (t) cc_final: 0.8335 (p) REVERT: C 1139 ASP cc_start: 0.7360 (t0) cc_final: 0.7098 (t0) REVERT: D 282 THR cc_start: 0.2821 (p) cc_final: 0.2340 (p) REVERT: D 429 GLN cc_start: 0.6465 (mm110) cc_final: 0.6195 (pp30) REVERT: D 474 MET cc_start: 0.5026 (mmm) cc_final: 0.4798 (mmm) outliers start: 85 outliers final: 67 residues processed: 319 average time/residue: 0.1691 time to fit residues: 90.3544 Evaluate side-chains 301 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 209 optimal weight: 0.0060 chunk 178 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 327 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 907 ASN B1119 ASN C 978 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 535 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.130271 restraints weight = 62968.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126447 restraints weight = 93504.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124381 restraints weight = 93468.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.124348 restraints weight = 89048.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123683 restraints weight = 72678.063| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29308 Z= 0.138 Angle : 0.651 20.103 39993 Z= 0.313 Chirality : 0.047 0.600 4676 Planarity : 0.004 0.050 5034 Dihedral : 5.754 59.660 5208 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 2.93 % Allowed : 13.72 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3432 helix: 1.17 (0.16), residues: 1032 sheet: -0.04 (0.19), residues: 648 loop : -0.74 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.023 0.001 TYR C1067 PHE 0.022 0.001 PHE A 400 TRP 0.020 0.001 TRP B1102 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00313 (29197) covalent geometry : angle 0.58927 (39703) SS BOND : bond 0.00393 ( 40) SS BOND : angle 1.89455 ( 80) hydrogen bonds : bond 0.03626 ( 1230) hydrogen bonds : angle 5.35582 ( 3438) Misc. bond : bond 0.00036 ( 1) link_BETA1-4 : bond 0.00509 ( 17) link_BETA1-4 : angle 1.75296 ( 51) link_NAG-ASN : bond 0.00813 ( 53) link_NAG-ASN : angle 4.12875 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 260 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4287 (OUTLIER) cc_final: 0.3478 (m170) REVERT: A 528 LYS cc_start: 0.6701 (ttpt) cc_final: 0.6408 (pttp) REVERT: A 869 MET cc_start: 0.7845 (mtp) cc_final: 0.7610 (mtp) REVERT: B 873 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: B 1075 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6276 (p90) REVERT: B 1135 ASN cc_start: 0.7636 (t0) cc_final: 0.7323 (t0) REVERT: C 305 SER cc_start: 0.8529 (t) cc_final: 0.8288 (p) REVERT: D 282 THR cc_start: 0.2822 (p) cc_final: 0.2342 (p) REVERT: D 429 GLN cc_start: 0.6410 (mm110) cc_final: 0.6140 (pp30) outliers start: 90 outliers final: 69 residues processed: 327 average time/residue: 0.1608 time to fit residues: 87.9608 Evaluate side-chains 310 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 214 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 315 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN B1119 ASN C 978 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.152016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127836 restraints weight = 64039.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.123576 restraints weight = 98473.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121822 restraints weight = 100273.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.121912 restraints weight = 85589.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121366 restraints weight = 68316.120| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29308 Z= 0.141 Angle : 0.651 21.111 39993 Z= 0.314 Chirality : 0.046 0.569 4676 Planarity : 0.004 0.049 5034 Dihedral : 5.646 59.997 5208 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 2.80 % Allowed : 14.24 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3432 helix: 1.23 (0.16), residues: 1032 sheet: -0.05 (0.19), residues: 655 loop : -0.70 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.023 0.001 TYR C1067 PHE 0.015 0.001 PHE A 65 TRP 0.017 0.001 TRP B1102 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00323 (29197) covalent geometry : angle 0.58761 (39703) SS BOND : bond 0.00395 ( 40) SS BOND : angle 2.13844 ( 80) hydrogen bonds : bond 0.03602 ( 1230) hydrogen bonds : angle 5.30634 ( 3438) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00481 ( 17) link_BETA1-4 : angle 1.70858 ( 51) link_NAG-ASN : bond 0.00787 ( 53) link_NAG-ASN : angle 4.14476 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.2201 (t80) cc_final: 0.1088 (m-10) REVERT: A 528 LYS cc_start: 0.6740 (ttpt) cc_final: 0.6502 (pttp) REVERT: B 873 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: B 1075 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6155 (p90) REVERT: B 1135 ASN cc_start: 0.7628 (t0) cc_final: 0.7366 (t0) REVERT: C 305 SER cc_start: 0.8535 (t) cc_final: 0.8290 (p) REVERT: D 282 THR cc_start: 0.3172 (p) cc_final: 0.2712 (p) REVERT: D 429 GLN cc_start: 0.6399 (mm110) cc_final: 0.6137 (pp30) outliers start: 86 outliers final: 76 residues processed: 321 average time/residue: 0.1641 time to fit residues: 88.8955 Evaluate side-chains 324 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 311 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 121 ASN B 872 GLN B1119 ASN C 978 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128122 restraints weight = 63967.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124967 restraints weight = 98517.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122078 restraints weight = 99464.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121948 restraints weight = 94038.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121111 restraints weight = 73595.156| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29308 Z= 0.166 Angle : 0.667 19.610 39993 Z= 0.324 Chirality : 0.047 0.501 4676 Planarity : 0.004 0.049 5034 Dihedral : 5.641 59.545 5207 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 2.89 % Allowed : 14.50 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3432 helix: 1.22 (0.16), residues: 1030 sheet: -0.06 (0.18), residues: 666 loop : -0.74 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.024 0.001 TYR C1067 PHE 0.018 0.001 PHE A1103 TRP 0.017 0.001 TRP B1102 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00386 (29197) covalent geometry : angle 0.60468 (39703) SS BOND : bond 0.00451 ( 40) SS BOND : angle 2.45748 ( 80) hydrogen bonds : bond 0.03668 ( 1230) hydrogen bonds : angle 5.34569 ( 3438) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00480 ( 17) link_BETA1-4 : angle 1.66031 ( 51) link_NAG-ASN : bond 0.00825 ( 53) link_NAG-ASN : angle 4.10251 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 241 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.2179 (t80) cc_final: 0.1155 (m-10) REVERT: A 528 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6475 (pttp) REVERT: B 873 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: B 1075 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6246 (p90) REVERT: B 1135 ASN cc_start: 0.7606 (t0) cc_final: 0.7386 (t0) REVERT: C 216 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7658 (mt) REVERT: C 305 SER cc_start: 0.8542 (t) cc_final: 0.8298 (p) REVERT: D 282 THR cc_start: 0.3293 (p) cc_final: 0.2831 (p) REVERT: D 429 GLN cc_start: 0.6323 (mm110) cc_final: 0.6083 (pp30) outliers start: 89 outliers final: 80 residues processed: 301 average time/residue: 0.1610 time to fit residues: 81.7137 Evaluate side-chains 317 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 234 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 149 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 293 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 203 optimal weight: 6.9990 chunk 271 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 163 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 872 GLN B1119 ASN C 978 ASN D 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.153179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.129157 restraints weight = 63710.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124991 restraints weight = 99929.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.122670 restraints weight = 99377.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122875 restraints weight = 84768.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122353 restraints weight = 65269.115| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29308 Z= 0.112 Angle : 0.631 21.010 39993 Z= 0.305 Chirality : 0.045 0.461 4676 Planarity : 0.004 0.047 5034 Dihedral : 5.357 59.709 5207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 1.82 % Allowed : 15.74 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3432 helix: 1.39 (0.17), residues: 1032 sheet: 0.09 (0.19), residues: 652 loop : -0.68 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.021 0.001 TYR C1067 PHE 0.023 0.001 PHE D 28 TRP 0.018 0.001 TRP B1102 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (29197) covalent geometry : angle 0.57077 (39703) SS BOND : bond 0.00274 ( 40) SS BOND : angle 2.08363 ( 80) hydrogen bonds : bond 0.03336 ( 1230) hydrogen bonds : angle 5.20793 ( 3438) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00490 ( 17) link_BETA1-4 : angle 1.63134 ( 51) link_NAG-ASN : bond 0.00781 ( 53) link_NAG-ASN : angle 3.98217 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.1818 (t80) cc_final: 0.0971 (m-10) REVERT: A 200 TYR cc_start: 0.4447 (m-80) cc_final: 0.4216 (m-80) REVERT: A 202 LYS cc_start: 0.5403 (mptt) cc_final: 0.4969 (tptt) REVERT: A 321 GLN cc_start: 0.7306 (mm-40) cc_final: 0.6956 (pt0) REVERT: B 873 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 1075 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6180 (p90) REVERT: B 1135 ASN cc_start: 0.7476 (t0) cc_final: 0.7254 (t0) REVERT: C 305 SER cc_start: 0.8444 (t) cc_final: 0.8191 (p) REVERT: D 282 THR cc_start: 0.3380 (p) cc_final: 0.2912 (p) REVERT: D 429 GLN cc_start: 0.6315 (mm110) cc_final: 0.6075 (pp30) outliers start: 56 outliers final: 45 residues processed: 311 average time/residue: 0.1657 time to fit residues: 85.8048 Evaluate side-chains 302 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 243 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 120 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 954 GLN B1119 ASN ** D 24 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.153976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127533 restraints weight = 62998.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.124069 restraints weight = 74310.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120899 restraints weight = 66812.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120241 restraints weight = 65683.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.119792 restraints weight = 51573.189| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29308 Z= 0.122 Angle : 0.643 18.725 39993 Z= 0.311 Chirality : 0.045 0.483 4676 Planarity : 0.004 0.047 5034 Dihedral : 5.288 59.438 5207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.85 % Allowed : 16.39 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3432 helix: 1.36 (0.16), residues: 1039 sheet: 0.05 (0.18), residues: 664 loop : -0.67 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 582 TYR 0.024 0.001 TYR D 83 PHE 0.041 0.001 PHE C 927 TRP 0.055 0.001 TRP A1102 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00275 (29197) covalent geometry : angle 0.58732 (39703) SS BOND : bond 0.00302 ( 40) SS BOND : angle 1.97040 ( 80) hydrogen bonds : bond 0.03377 ( 1230) hydrogen bonds : angle 5.18904 ( 3438) Misc. bond : bond 0.00034 ( 1) link_BETA1-4 : bond 0.00470 ( 17) link_BETA1-4 : angle 1.59409 ( 51) link_NAG-ASN : bond 0.00663 ( 53) link_NAG-ASN : angle 3.88198 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5118.30 seconds wall clock time: 89 minutes 17.26 seconds (5357.26 seconds total)