Starting phenix.real_space_refine on Sun Jul 5 00:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lws_23555/07_2026/7lws_23555.cif" } resolution = 3.22 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= 0.086 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 104 5.16 5 C 15489 2.51 5 N 3957 2.21 5 O 4770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24320 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7812 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7813 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7813 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 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 chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.89, per 1000 atoms: 0.24 Number of scatterers: 24320 At special positions: 0 Unit cell: (130.418, 138.97, 176.385, 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 104 16.00 O 4770 8.00 N 3957 7.00 C 15489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 709 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 26.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.742A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.645A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.859A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.196A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.002A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.570A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.524A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.103A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.536A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.628A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.563A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.359A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.671A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.858A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.749A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.806A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.552A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.891A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.715A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.754A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 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: 3.671A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.004A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' 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: 3.713A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.548A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.933A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.627A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.550A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.551A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.590A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.631A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 948 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 4.159A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.294A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.132A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.207A 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: 5.406A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.798A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.670A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.858A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.875A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.857A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.804A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.491A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.078A pdb=" N GLN A1071 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.541A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.207A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.807A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.891A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.744A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.677A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 313 through 318 removed outlier: 5.634A pdb=" N GLN B 314 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 599 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 316 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.745A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.653A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.713A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.713A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.586A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.067A 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: 3.775A 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 removed outlier: 5.274A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.883A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.638A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.466A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.929A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.965A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.727A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6145 1.33 - 1.46: 4823 1.46 - 1.58: 13746 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 24842 Sorted by residual: bond pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 1.409 1.496 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.487 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 29495 2.76 - 5.52: 4165 5.52 - 8.27: 116 8.27 - 11.03: 6 11.03 - 13.79: 3 Bond angle restraints: 33785 Sorted by residual: angle pdb=" CA ASP A1041 " pdb=" CB ASP A1041 " pdb=" CG ASP A1041 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASN A 777 " pdb=" CB ASN A 777 " pdb=" CG ASN A 777 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" C GLY B 381 " pdb=" N VAL B 382 " pdb=" CA VAL B 382 " ideal model delta sigma weight residual 122.23 130.29 -8.06 1.44e+00 4.82e-01 3.13e+01 angle pdb=" CA GLY B 416 " pdb=" C GLY B 416 " pdb=" N LYS B 417 " ideal model delta sigma weight residual 114.23 119.09 -4.86 8.80e-01 1.29e+00 3.05e+01 angle pdb=" OE1 GLN C 926 " pdb=" CD GLN C 926 " pdb=" NE2 GLN C 926 " ideal model delta sigma weight residual 122.60 117.26 5.34 1.00e+00 1.00e+00 2.85e+01 ... (remaining 33780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13265 17.97 - 35.94: 812 35.94 - 53.91: 117 53.91 - 71.88: 53 71.88 - 89.85: 26 Dihedral angle restraints: 14273 sinusoidal: 5552 harmonic: 8721 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.74 75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.35 64.35 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 14270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 4009 0.284 - 0.569: 22 0.569 - 0.853: 0 0.853 - 1.137: 0 1.137 - 1.422: 4 Chirality restraints: 4035 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.88e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.85e+01 ... (remaining 4032 not shown) Planarity restraints: 4326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.122 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" CG ASN B 657 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.193 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.118 2.00e-02 2.50e+03 1.27e-01 2.00e+02 pdb=" CG ASN C 234 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.197 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.108 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN C 331 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.172 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.132 2.00e-02 2.50e+03 ... (remaining 4323 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11842 2.99 - 3.47: 22781 3.47 - 3.95: 39280 3.95 - 4.42: 43772 4.42 - 4.90: 74777 Nonbonded interactions: 192452 Sorted by model distance: nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.517 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.520 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.532 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.535 3.040 ... (remaining 192447 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 1308) selection = (chain 'B' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1308)) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 25.260 Find NCS groups from input model: 1.000 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.014 0.087 24943 Z= 0.801 Angle : 1.833 19.565 34050 Z= 1.201 Chirality : 0.109 1.422 4035 Planarity : 0.013 0.206 4281 Dihedral : 13.133 89.850 8543 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.65 % Favored : 95.01 % Rotamer: Outliers : 0.95 % Allowed : 2.56 % Favored : 96.49 % Cbeta Deviations : 0.14 % 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: -1.08 (0.14), residues: 2946 helix: -1.60 (0.16), residues: 656 sheet: 0.53 (0.21), residues: 534 loop : -0.72 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 319 TYR 0.160 0.019 TYR A 904 PHE 0.086 0.011 PHE A 718 TRP 0.123 0.026 TRP A 886 HIS 0.012 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01402 / 0.80 (24842) covalent geometry : angle 1.79742 / 1.20 (33785) SS BOND : bond 0.01293 / 0.83 ( 38) SS BOND : angle 2.27905 / 1.47 ( 76) hydrogen bonds : bond 0.16587 / 11.02 ( 1011) hydrogen bonds : angle 8.49816 / 5.92 ( 2763) link_BETA1-4 : bond 0.03090 / 1.81 ( 18) link_BETA1-4 : angle 6.04106 / 3.68 ( 54) link_NAG-ASN : bond 0.01494 / 0.98 ( 45) link_NAG-ASN : angle 4.67412 / 3.21 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9227 (mt) cc_final: 0.9014 (mp) REVERT: A 88 ASP cc_start: 0.7891 (m-30) cc_final: 0.7653 (m-30) REVERT: A 99 ASN cc_start: 0.7180 (m-40) cc_final: 0.6493 (m110) REVERT: A 115 GLN cc_start: 0.6646 (mp10) cc_final: 0.6353 (mp10) REVERT: A 128 ILE cc_start: 0.7654 (mt) cc_final: 0.7417 (mp) REVERT: A 202 LYS cc_start: 0.7720 (mttm) cc_final: 0.7459 (mttp) REVERT: A 237 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6441 (mtm-85) REVERT: A 389 ASP cc_start: 0.8058 (m-30) cc_final: 0.7812 (t0) REVERT: A 400 PHE cc_start: 0.8475 (p90) cc_final: 0.8247 (p90) REVERT: A 673 SER cc_start: 0.8106 (p) cc_final: 0.7855 (p) REVERT: A 740 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: A 869 MET cc_start: 0.8845 (mtm) cc_final: 0.8610 (mtp) REVERT: A 886 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.7231 (m-90) REVERT: A 1128 VAL cc_start: 0.8660 (t) cc_final: 0.8266 (p) REVERT: B 127 VAL cc_start: 0.7718 (t) cc_final: 0.7405 (p) REVERT: B 133 PHE cc_start: 0.7248 (m-80) cc_final: 0.6822 (m-80) REVERT: B 581 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.5888 (m) REVERT: B 646 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7677 (tpm170) REVERT: B 740 MET cc_start: 0.8513 (tpt) cc_final: 0.7730 (tpt) REVERT: B 902 MET cc_start: 0.8552 (mmm) cc_final: 0.8196 (mmm) REVERT: C 64 TRP cc_start: 0.7428 (t60) cc_final: 0.7153 (t60) REVERT: C 81 ASN cc_start: 0.7989 (p0) cc_final: 0.7774 (p0) REVERT: C 207 HIS cc_start: 0.7443 (m-70) cc_final: 0.7212 (m-70) REVERT: C 271 GLN cc_start: 0.7986 (mt0) cc_final: 0.7742 (mm-40) REVERT: C 374 PHE cc_start: 0.7164 (m-80) cc_final: 0.6920 (m-80) REVERT: C 422 ASN cc_start: 0.7185 (m-40) cc_final: 0.6136 (t0) REVERT: C 453 TYR cc_start: 0.5165 (p90) cc_final: 0.4922 (p90) REVERT: C 581 THR cc_start: 0.6641 (m) cc_final: 0.6367 (p) REVERT: C 780 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7618 (mm-30) outliers start: 25 outliers final: 8 residues processed: 391 average time/residue: 0.1803 time to fit residues: 110.0732 Evaluate side-chains 212 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 777 ASN A 925 ASN A 960 ASN B 188 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 907 ASN B 920 GLN B 953 ASN C 134 GLN C 394 ASN C1010 GLN C1088 HIS C1118 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116467 restraints weight = 33053.432| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.77 r_work: 0.3142 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24943 Z= 0.145 Angle : 0.717 16.821 34050 Z= 0.361 Chirality : 0.049 0.445 4035 Planarity : 0.004 0.050 4281 Dihedral : 6.394 56.513 3217 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 1.60 % Allowed : 5.69 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.08 (0.15), residues: 2946 helix: 0.66 (0.20), residues: 651 sheet: 0.41 (0.19), residues: 679 loop : -0.51 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.026 0.002 TYR B 369 PHE 0.024 0.002 PHE B 168 TRP 0.014 0.001 TRP B 64 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (24842) covalent geometry : angle 0.67649 / 0.35 (33785) SS BOND : bond 0.00357 / 0.27 ( 38) SS BOND : angle 1.02232 / 0.62 ( 76) hydrogen bonds : bond 0.04874 / 3.10 ( 1011) hydrogen bonds : angle 6.26494 / 4.38 ( 2763) link_BETA1-4 : bond 0.01134 / 0.81 ( 18) link_BETA1-4 : angle 3.42318 / 2.03 ( 54) link_NAG-ASN : bond 0.00493 / 0.33 ( 45) link_NAG-ASN : angle 3.14255 / 2.14 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.5713 (m-10) cc_final: 0.5443 (m-10) REVERT: A 202 LYS cc_start: 0.7800 (mttm) cc_final: 0.7546 (mttp) REVERT: A 389 ASP cc_start: 0.8410 (m-30) cc_final: 0.8036 (t0) REVERT: A 574 ASP cc_start: 0.7573 (t0) cc_final: 0.7000 (t0) REVERT: A 646 ARG cc_start: 0.8805 (ttt180) cc_final: 0.8557 (ttm110) REVERT: B 81 ASN cc_start: 0.8167 (p0) cc_final: 0.7847 (p0) REVERT: B 131 CYS cc_start: 0.5962 (m) cc_final: 0.5685 (m) REVERT: B 133 PHE cc_start: 0.7341 (m-80) cc_final: 0.6807 (m-80) REVERT: B 396 TYR cc_start: 0.5467 (m-80) cc_final: 0.5041 (m-10) REVERT: B 505 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.5870 (t80) REVERT: B 646 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.7803 (tpt170) REVERT: B 814 LYS cc_start: 0.8508 (mttt) cc_final: 0.8272 (mtmt) REVERT: B 902 MET cc_start: 0.8626 (mmm) cc_final: 0.8273 (tpt) REVERT: B 957 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8137 (tt0) REVERT: C 64 TRP cc_start: 0.7418 (t60) cc_final: 0.7069 (t60) REVERT: C 81 ASN cc_start: 0.8113 (p0) cc_final: 0.7773 (p0) REVERT: C 170 TYR cc_start: 0.7945 (t80) cc_final: 0.7700 (t80) REVERT: C 205 SER cc_start: 0.8638 (p) cc_final: 0.8173 (t) REVERT: C 207 HIS cc_start: 0.7467 (m-70) cc_final: 0.7262 (m-70) REVERT: C 278 LYS cc_start: 0.7922 (tttt) cc_final: 0.7655 (tttp) REVERT: C 374 PHE cc_start: 0.7206 (m-80) cc_final: 0.6991 (m-80) REVERT: C 780 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8164 (mm-30) outliers start: 42 outliers final: 21 residues processed: 273 average time/residue: 0.1721 time to fit residues: 75.0964 Evaluate side-chains 205 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 233 optimal weight: 5.9990 chunk 284 optimal weight: 0.0770 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 960 ASN A1048 HIS B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116735 restraints weight = 32854.345| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.69 r_work: 0.3145 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24943 Z= 0.121 Angle : 0.620 17.077 34050 Z= 0.309 Chirality : 0.047 0.395 4035 Planarity : 0.004 0.044 4281 Dihedral : 5.632 58.042 3212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 2.06 % Allowed : 7.26 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.24 (0.15), residues: 2946 helix: 1.32 (0.21), residues: 640 sheet: 0.31 (0.19), residues: 679 loop : -0.33 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.022 0.001 TYR A 380 PHE 0.020 0.001 PHE C 192 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24842) covalent geometry : angle 0.58554 / 0.30 (33785) SS BOND : bond 0.00310 / 0.19 ( 38) SS BOND : angle 1.00492 / 0.63 ( 76) hydrogen bonds : bond 0.04203 / 2.66 ( 1011) hydrogen bonds : angle 5.77029 / 4.03 ( 2763) link_BETA1-4 : bond 0.01248 / 0.91 ( 18) link_BETA1-4 : angle 3.18043 / 1.83 ( 54) link_NAG-ASN : bond 0.00434 / 0.28 ( 45) link_NAG-ASN : angle 2.55756 / 1.70 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.916 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: A 170 TYR cc_start: 0.7448 (t80) cc_final: 0.7232 (t80) REVERT: A 200 TYR cc_start: 0.5408 (m-10) cc_final: 0.4978 (m-10) REVERT: A 202 LYS cc_start: 0.7969 (mttm) cc_final: 0.7749 (mttp) REVERT: A 218 GLN cc_start: 0.8181 (pp30) cc_final: 0.7978 (pp30) REVERT: A 237 ARG cc_start: 0.7356 (mtt90) cc_final: 0.6933 (ttp-110) REVERT: A 313 TYR cc_start: 0.8779 (m-80) cc_final: 0.8508 (m-80) REVERT: A 389 ASP cc_start: 0.8530 (m-30) cc_final: 0.7968 (t0) REVERT: A 465 GLU cc_start: 0.7630 (tt0) cc_final: 0.7393 (tt0) REVERT: A 574 ASP cc_start: 0.7769 (t0) cc_final: 0.7259 (t0) REVERT: A 646 ARG cc_start: 0.9015 (ttt180) cc_final: 0.8758 (ttm110) REVERT: B 81 ASN cc_start: 0.8316 (p0) cc_final: 0.7934 (p0) REVERT: B 117 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7861 (mm) REVERT: B 131 CYS cc_start: 0.6469 (m) cc_final: 0.6267 (m) REVERT: B 396 TYR cc_start: 0.5790 (m-80) cc_final: 0.5293 (m-10) REVERT: B 505 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.5650 (t80) REVERT: B 646 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.7869 (tpt170) REVERT: B 814 LYS cc_start: 0.8461 (mttt) cc_final: 0.8194 (mtmt) REVERT: B 902 MET cc_start: 0.8751 (mmm) cc_final: 0.8406 (tpt) REVERT: B 957 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8251 (tt0) REVERT: B 988 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7994 (mt-10) REVERT: B 994 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: C 64 TRP cc_start: 0.7550 (t60) cc_final: 0.7211 (t60) REVERT: C 81 ASN cc_start: 0.8247 (p0) cc_final: 0.7895 (p0) REVERT: C 368 LEU cc_start: 0.8485 (mp) cc_final: 0.8260 (mp) REVERT: C 780 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8435 (mm-30) outliers start: 54 outliers final: 33 residues processed: 250 average time/residue: 0.1525 time to fit residues: 63.1527 Evaluate side-chains 209 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 91 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 273 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117014 restraints weight = 32787.396| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.71 r_work: 0.3157 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24943 Z= 0.116 Angle : 0.583 16.744 34050 Z= 0.290 Chirality : 0.046 0.393 4035 Planarity : 0.004 0.042 4281 Dihedral : 5.230 59.594 3210 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 8.79 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.35 (0.15), residues: 2946 helix: 1.43 (0.21), residues: 658 sheet: 0.33 (0.19), residues: 681 loop : -0.26 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.030 0.001 TYR A 380 PHE 0.019 0.001 PHE B 133 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (24842) covalent geometry : angle 0.55092 / 0.28 (33785) SS BOND : bond 0.00317 / 0.23 ( 38) SS BOND : angle 1.19742 / 0.74 ( 76) hydrogen bonds : bond 0.03796 / 2.42 ( 1011) hydrogen bonds : angle 5.52094 / 3.88 ( 2763) link_BETA1-4 : bond 0.01151 / 0.84 ( 18) link_BETA1-4 : angle 3.05179 / 1.75 ( 54) link_NAG-ASN : bond 0.00390 / 0.26 ( 45) link_NAG-ASN : angle 2.31629 / 1.52 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 0.985 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 115 GLN cc_start: 0.7511 (tt0) cc_final: 0.7141 (tp-100) REVERT: A 170 TYR cc_start: 0.7456 (t80) cc_final: 0.7173 (t80) REVERT: A 200 TYR cc_start: 0.5335 (m-10) cc_final: 0.4916 (m-10) REVERT: A 237 ARG cc_start: 0.7330 (mtt90) cc_final: 0.6912 (ttp-110) REVERT: A 389 ASP cc_start: 0.8433 (m-30) cc_final: 0.7992 (t0) REVERT: A 422 ASN cc_start: 0.7510 (m110) cc_final: 0.7105 (m110) REVERT: A 646 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8756 (ttm110) REVERT: A 1114 ILE cc_start: 0.9073 (mm) cc_final: 0.8689 (tp) REVERT: B 81 ASN cc_start: 0.8378 (p0) cc_final: 0.8021 (p0) REVERT: B 117 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7817 (mm) REVERT: B 131 CYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6285 (m) REVERT: B 133 PHE cc_start: 0.7691 (m-80) cc_final: 0.7404 (m-80) REVERT: B 228 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6856 (t0) REVERT: B 396 TYR cc_start: 0.6093 (m-80) cc_final: 0.5558 (m-10) REVERT: B 814 LYS cc_start: 0.8393 (mttt) cc_final: 0.8145 (mtmt) REVERT: B 902 MET cc_start: 0.8725 (mmm) cc_final: 0.8475 (tpt) REVERT: B 904 TYR cc_start: 0.8375 (m-10) cc_final: 0.7969 (m-10) REVERT: B 988 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8138 (mt-10) REVERT: B 994 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: C 81 ASN cc_start: 0.8304 (p0) cc_final: 0.7942 (p0) REVERT: C 187 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6795 (tptp) REVERT: C 357 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7307 (mtt-85) REVERT: C 780 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8350 (mm-30) REVERT: C 855 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7822 (t80) outliers start: 55 outliers final: 36 residues processed: 240 average time/residue: 0.1590 time to fit residues: 62.9847 Evaluate side-chains 214 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 73 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1101 HIS C 207 HIS C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.171207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113487 restraints weight = 32590.624| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.03 r_work: 0.3118 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24943 Z= 0.205 Angle : 0.644 16.693 34050 Z= 0.321 Chirality : 0.048 0.388 4035 Planarity : 0.004 0.047 4281 Dihedral : 5.263 47.399 3208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.41 % Allowed : 9.47 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 2946 helix: 1.32 (0.21), residues: 654 sheet: 0.22 (0.19), residues: 675 loop : -0.42 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.020 0.002 TYR B 170 PHE 0.020 0.002 PHE A1121 TRP 0.009 0.001 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.20 (24842) covalent geometry : angle 0.61355 / 0.31 (33785) SS BOND : bond 0.00381 / 0.26 ( 38) SS BOND : angle 1.45675 / 0.95 ( 76) hydrogen bonds : bond 0.04491 / 2.91 ( 1011) hydrogen bonds : angle 5.71318 / 4.01 ( 2763) link_BETA1-4 : bond 0.01042 / 0.76 ( 18) link_BETA1-4 : angle 3.10005 / 1.78 ( 54) link_NAG-ASN : bond 0.00358 / 0.23 ( 45) link_NAG-ASN : angle 2.32646 / 1.54 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 0.941 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: A 115 GLN cc_start: 0.7631 (tt0) cc_final: 0.7220 (tp-100) REVERT: A 237 ARG cc_start: 0.7429 (mtt90) cc_final: 0.6784 (mtm-85) REVERT: A 389 ASP cc_start: 0.8472 (m-30) cc_final: 0.8083 (t0) REVERT: A 646 ARG cc_start: 0.9030 (ttt180) cc_final: 0.8793 (ttm110) REVERT: A 1114 ILE cc_start: 0.9100 (mm) cc_final: 0.8719 (tp) REVERT: B 81 ASN cc_start: 0.8509 (p0) cc_final: 0.8210 (p0) REVERT: B 131 CYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6169 (m) REVERT: B 133 PHE cc_start: 0.7662 (m-80) cc_final: 0.7361 (m-80) REVERT: B 316 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8369 (m) REVERT: B 396 TYR cc_start: 0.6159 (m-80) cc_final: 0.5602 (m-10) REVERT: B 814 LYS cc_start: 0.8389 (mttt) cc_final: 0.8153 (mtmt) REVERT: B 902 MET cc_start: 0.8689 (mmm) cc_final: 0.8484 (tpt) REVERT: B 988 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8097 (mt-10) REVERT: C 81 ASN cc_start: 0.8385 (p0) cc_final: 0.7988 (p0) REVERT: C 187 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6816 (tptp) REVERT: C 357 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7420 (mtt-85) REVERT: C 855 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7964 (t80) outliers start: 63 outliers final: 44 residues processed: 228 average time/residue: 0.1341 time to fit residues: 51.2189 Evaluate side-chains 217 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 295 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 422 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 207 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112619 restraints weight = 32846.086| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.68 r_work: 0.3081 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24943 Z= 0.165 Angle : 0.600 16.780 34050 Z= 0.298 Chirality : 0.046 0.389 4035 Planarity : 0.004 0.049 4281 Dihedral : 5.104 50.879 3207 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 9.97 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.15), residues: 2946 helix: 1.37 (0.21), residues: 658 sheet: 0.21 (0.19), residues: 662 loop : -0.43 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 357 TYR 0.019 0.001 TYR B 170 PHE 0.022 0.001 PHE A 855 TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (24842) covalent geometry : angle 0.57036 / 0.29 (33785) SS BOND : bond 0.00384 / 0.28 ( 38) SS BOND : angle 1.34548 / 0.89 ( 76) hydrogen bonds : bond 0.04114 / 2.65 ( 1011) hydrogen bonds : angle 5.62347 / 3.95 ( 2763) link_BETA1-4 : bond 0.01125 / 0.83 ( 18) link_BETA1-4 : angle 3.05610 / 1.75 ( 54) link_NAG-ASN : bond 0.00346 / 0.23 ( 45) link_NAG-ASN : angle 2.16466 / 1.43 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 0.919 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: A 115 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7064 (tp-100) REVERT: A 237 ARG cc_start: 0.7411 (mtt90) cc_final: 0.6788 (mtm-85) REVERT: A 357 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7340 (ttm110) REVERT: A 389 ASP cc_start: 0.8535 (m-30) cc_final: 0.8145 (t0) REVERT: A 646 ARG cc_start: 0.9070 (ttt180) cc_final: 0.8847 (ttm110) REVERT: A 1072 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: A 1114 ILE cc_start: 0.9088 (mm) cc_final: 0.8734 (tp) REVERT: B 81 ASN cc_start: 0.8464 (p0) cc_final: 0.8209 (p0) REVERT: B 131 CYS cc_start: 0.6517 (OUTLIER) cc_final: 0.6263 (m) REVERT: B 133 PHE cc_start: 0.7618 (m-80) cc_final: 0.7312 (m-80) REVERT: B 316 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 396 TYR cc_start: 0.6345 (m-80) cc_final: 0.5733 (m-10) REVERT: B 562 PHE cc_start: 0.6471 (p90) cc_final: 0.6221 (p90) REVERT: B 814 LYS cc_start: 0.8402 (mttt) cc_final: 0.8151 (mtmt) REVERT: B 904 TYR cc_start: 0.8427 (m-10) cc_final: 0.8076 (m-10) REVERT: B 988 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8124 (mt-10) REVERT: C 81 ASN cc_start: 0.8395 (p0) cc_final: 0.7987 (p0) REVERT: C 187 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6812 (tptp) REVERT: C 207 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6662 (m90) REVERT: C 271 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8189 (mm-40) REVERT: C 855 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7983 (t80) outliers start: 65 outliers final: 52 residues processed: 234 average time/residue: 0.1481 time to fit residues: 58.0511 Evaluate side-chains 226 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 191 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 150 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 935 GLN B 196 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113279 restraints weight = 32695.772| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.72 r_work: 0.3108 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24943 Z= 0.116 Angle : 0.572 16.761 34050 Z= 0.283 Chirality : 0.045 0.390 4035 Planarity : 0.004 0.045 4281 Dihedral : 4.941 52.117 3207 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 10.54 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.16), residues: 2946 helix: 1.58 (0.21), residues: 658 sheet: 0.36 (0.19), residues: 672 loop : -0.35 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.019 0.001 TYR B 369 PHE 0.013 0.001 PHE A1121 TRP 0.015 0.001 TRP C 64 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (24842) covalent geometry : angle 0.54200 / 0.28 (33785) SS BOND : bond 0.00446 / 0.33 ( 38) SS BOND : angle 1.35918 / 0.87 ( 76) hydrogen bonds : bond 0.03727 / 2.38 ( 1011) hydrogen bonds : angle 5.50884 / 3.87 ( 2763) link_BETA1-4 : bond 0.01130 / 0.82 ( 18) link_BETA1-4 : angle 2.99986 / 1.72 ( 54) link_NAG-ASN : bond 0.00336 / 0.22 ( 45) link_NAG-ASN : angle 2.05484 / 1.34 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.873 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: A 115 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7431 (tp-100) REVERT: A 170 TYR cc_start: 0.7168 (t80) cc_final: 0.6785 (t80) REVERT: A 357 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7350 (ttm110) REVERT: A 389 ASP cc_start: 0.8529 (m-30) cc_final: 0.8138 (t0) REVERT: A 646 ARG cc_start: 0.9058 (ttt180) cc_final: 0.8831 (ttm110) REVERT: A 1072 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 1114 ILE cc_start: 0.9098 (mm) cc_final: 0.8727 (tp) REVERT: B 81 ASN cc_start: 0.8447 (p0) cc_final: 0.8207 (p0) REVERT: B 131 CYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5452 (m) REVERT: B 133 PHE cc_start: 0.7560 (m-80) cc_final: 0.5844 (t80) REVERT: B 316 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8478 (m) REVERT: B 396 TYR cc_start: 0.6371 (m-80) cc_final: 0.5668 (m-10) REVERT: B 814 LYS cc_start: 0.8390 (mttt) cc_final: 0.8144 (mtmt) REVERT: B 904 TYR cc_start: 0.8426 (m-10) cc_final: 0.8062 (m-10) REVERT: B 988 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8104 (mt-10) REVERT: C 81 ASN cc_start: 0.8406 (p0) cc_final: 0.8001 (p0) REVERT: C 187 LYS cc_start: 0.7026 (mmtt) cc_final: 0.6759 (tptp) REVERT: C 780 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8542 (mm-30) outliers start: 60 outliers final: 49 residues processed: 230 average time/residue: 0.1426 time to fit residues: 54.7618 Evaluate side-chains 220 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 72 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 139 optimal weight: 0.0000 chunk 174 optimal weight: 2.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 493 GLN B 394 ASN C 207 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110494 restraints weight = 32574.291| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.70 r_work: 0.3087 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24943 Z= 0.169 Angle : 0.602 16.737 34050 Z= 0.298 Chirality : 0.046 0.387 4035 Planarity : 0.004 0.049 4281 Dihedral : 4.963 50.035 3207 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.52 % Allowed : 10.54 % Favored : 86.94 % 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: 0.25 (0.16), residues: 2946 helix: 1.52 (0.21), residues: 658 sheet: 0.30 (0.19), residues: 664 loop : -0.42 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.017 0.001 TYR B 369 PHE 0.018 0.001 PHE A1121 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (24842) covalent geometry : angle 0.57301 / 0.29 (33785) SS BOND : bond 0.00380 / 0.28 ( 38) SS BOND : angle 1.45285 / 0.87 ( 76) hydrogen bonds : bond 0.04032 / 2.60 ( 1011) hydrogen bonds : angle 5.55463 / 3.89 ( 2763) link_BETA1-4 : bond 0.01128 / 0.82 ( 18) link_BETA1-4 : angle 3.04479 / 1.75 ( 54) link_NAG-ASN : bond 0.00330 / 0.22 ( 45) link_NAG-ASN : angle 2.06598 / 1.36 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 0.917 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: A 115 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: A 237 ARG cc_start: 0.7485 (mtt90) cc_final: 0.6786 (mtm-85) REVERT: A 389 ASP cc_start: 0.8642 (m-30) cc_final: 0.8181 (t0) REVERT: A 646 ARG cc_start: 0.9072 (ttt180) cc_final: 0.8840 (ttm110) REVERT: A 1072 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: A 1114 ILE cc_start: 0.9101 (mm) cc_final: 0.8734 (tp) REVERT: B 81 ASN cc_start: 0.8456 (p0) cc_final: 0.8229 (p0) REVERT: B 131 CYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5537 (m) REVERT: B 133 PHE cc_start: 0.7577 (m-80) cc_final: 0.5861 (t80) REVERT: B 316 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 396 TYR cc_start: 0.6353 (m-80) cc_final: 0.5622 (m-10) REVERT: B 814 LYS cc_start: 0.8430 (mttt) cc_final: 0.8166 (mtmt) REVERT: B 988 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8111 (mt-10) REVERT: C 81 ASN cc_start: 0.8436 (p0) cc_final: 0.8025 (p0) REVERT: C 187 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6786 (tptp) REVERT: C 271 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7887 (mm-40) outliers start: 66 outliers final: 54 residues processed: 225 average time/residue: 0.1407 time to fit residues: 53.2340 Evaluate side-chains 227 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 292 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113736 restraints weight = 32819.553| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.72 r_work: 0.3096 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24943 Z= 0.123 Angle : 0.580 16.759 34050 Z= 0.287 Chirality : 0.045 0.390 4035 Planarity : 0.004 0.061 4281 Dihedral : 4.897 49.964 3207 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.29 % Allowed : 10.96 % Favored : 86.75 % 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: 0.34 (0.16), residues: 2946 helix: 1.66 (0.21), residues: 658 sheet: 0.39 (0.19), residues: 644 loop : -0.40 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 357 TYR 0.018 0.001 TYR A 453 PHE 0.014 0.001 PHE A1121 TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (24842) covalent geometry : angle 0.55067 / 0.28 (33785) SS BOND : bond 0.00320 / 0.23 ( 38) SS BOND : angle 1.54070 / 0.94 ( 76) hydrogen bonds : bond 0.03756 / 2.41 ( 1011) hydrogen bonds : angle 5.48196 / 3.83 ( 2763) link_BETA1-4 : bond 0.01146 / 0.83 ( 18) link_BETA1-4 : angle 2.99547 / 1.72 ( 54) link_NAG-ASN : bond 0.00326 / 0.22 ( 45) link_NAG-ASN : angle 1.98282 / 1.30 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.910 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: A 115 GLN cc_start: 0.7765 (tt0) cc_final: 0.7449 (tp40) REVERT: A 357 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7089 (ttm110) REVERT: A 389 ASP cc_start: 0.8474 (m-30) cc_final: 0.8069 (t0) REVERT: A 646 ARG cc_start: 0.8957 (ttt180) cc_final: 0.8749 (ttm110) REVERT: A 1072 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: A 1114 ILE cc_start: 0.9072 (mm) cc_final: 0.8709 (tp) REVERT: B 131 CYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5207 (m) REVERT: B 133 PHE cc_start: 0.7540 (m-80) cc_final: 0.5862 (t80) REVERT: B 316 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 396 TYR cc_start: 0.6344 (m-80) cc_final: 0.5564 (m-10) REVERT: B 902 MET cc_start: 0.8587 (tpt) cc_final: 0.8169 (tpt) REVERT: B 904 TYR cc_start: 0.8176 (m-10) cc_final: 0.7796 (m-10) REVERT: B 988 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8043 (mt-10) REVERT: B 1050 MET cc_start: 0.8835 (mtm) cc_final: 0.8633 (mtm) REVERT: C 81 ASN cc_start: 0.8421 (p0) cc_final: 0.8018 (p0) REVERT: C 271 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 780 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8282 (mm-30) outliers start: 60 outliers final: 53 residues processed: 226 average time/residue: 0.1407 time to fit residues: 53.9125 Evaluate side-chains 224 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 131 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN B 935 GLN C 207 HIS C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113069 restraints weight = 32755.560| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.10 r_work: 0.3115 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24943 Z= 0.188 Angle : 0.624 16.688 34050 Z= 0.310 Chirality : 0.047 0.384 4035 Planarity : 0.004 0.060 4281 Dihedral : 4.987 46.193 3206 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 11.19 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2946 helix: 1.49 (0.21), residues: 658 sheet: 0.32 (0.19), residues: 643 loop : -0.50 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 357 TYR 0.017 0.001 TYR A 453 PHE 0.020 0.001 PHE A1121 TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (24842) covalent geometry : angle 0.59445 / 0.30 (33785) SS BOND : bond 0.00397 / 0.29 ( 38) SS BOND : angle 1.82559 / 1.14 ( 76) hydrogen bonds : bond 0.04192 / 2.72 ( 1011) hydrogen bonds : angle 5.59367 / 3.91 ( 2763) link_BETA1-4 : bond 0.01075 / 0.78 ( 18) link_BETA1-4 : angle 3.03557 / 1.74 ( 54) link_NAG-ASN : bond 0.00330 / 0.21 ( 45) link_NAG-ASN : angle 2.05033 / 1.36 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 0.948 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 115 GLN cc_start: 0.7888 (tt0) cc_final: 0.7455 (tp-100) REVERT: A 237 ARG cc_start: 0.7457 (mtt90) cc_final: 0.6735 (mtm-85) REVERT: A 357 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7241 (ttm110) REVERT: A 389 ASP cc_start: 0.8611 (m-30) cc_final: 0.8134 (t0) REVERT: A 646 ARG cc_start: 0.9039 (ttt180) cc_final: 0.8407 (tpt170) REVERT: A 1072 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: A 1114 ILE cc_start: 0.9077 (mm) cc_final: 0.8698 (tp) REVERT: B 131 CYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5423 (m) REVERT: B 133 PHE cc_start: 0.7606 (m-80) cc_final: 0.5888 (t80) REVERT: B 316 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8427 (m) REVERT: B 396 TYR cc_start: 0.6439 (m-80) cc_final: 0.5556 (m-10) REVERT: B 529 LYS cc_start: 0.8848 (mttt) cc_final: 0.8498 (mtmm) REVERT: B 988 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8039 (mt-10) REVERT: C 81 ASN cc_start: 0.8432 (p0) cc_final: 0.8012 (p0) REVERT: C 207 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6701 (m90) REVERT: C 271 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7920 (mm-40) outliers start: 64 outliers final: 49 residues processed: 224 average time/residue: 0.1413 time to fit residues: 53.3232 Evaluate side-chains 221 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 220 optimal weight: 0.0040 chunk 275 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 394 ASN B 935 GLN C 207 HIS C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115606 restraints weight = 32751.771| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.97 r_work: 0.3147 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24943 Z= 0.110 Angle : 0.574 16.784 34050 Z= 0.285 Chirality : 0.045 0.392 4035 Planarity : 0.004 0.059 4281 Dihedral : 4.813 46.543 3206 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 1.91 % Allowed : 11.65 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.16), residues: 2946 helix: 1.71 (0.21), residues: 658 sheet: 0.35 (0.19), residues: 656 loop : -0.41 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 357 TYR 0.018 0.001 TYR A 453 PHE 0.011 0.001 PHE A1121 TRP 0.015 0.001 TRP C 64 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24842) covalent geometry : angle 0.54564 / 0.28 (33785) SS BOND : bond 0.00308 / 0.23 ( 38) SS BOND : angle 1.45748 / 0.89 ( 76) hydrogen bonds : bond 0.03662 / 2.35 ( 1011) hydrogen bonds : angle 5.44931 / 3.81 ( 2763) link_BETA1-4 : bond 0.01133 / 0.83 ( 18) link_BETA1-4 : angle 2.98327 / 1.71 ( 54) link_NAG-ASN : bond 0.00322 / 0.21 ( 45) link_NAG-ASN : angle 1.92452 / 1.26 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6942.82 seconds wall clock time: 119 minutes 28.50 seconds (7168.50 seconds total)