Starting phenix.real_space_refine on Sun Jul 5 10:22:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg7_32479/07_2026/7wg7_32479.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 17235 2.51 5 N 4408 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s 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: 27041 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 58, 'TRANS': 1039} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1038} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8770 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1057} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.11, per 1000 atoms: 0.19 Number of scatterers: 27041 At special positions: 0 Unit cell: (146.59, 147.66, 216.14, 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 118 16.00 O 5280 8.00 N 4408 7.00 C 17235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 125 " " NAG B1303 " - " ASN B 17 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 145 " " NAG C1303 " - " ASN C 17 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 717 " " NAG C1311 " - " ASN C 709 " " NAG D 1 " - " ASN B 233 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN A 233 " " NAG L 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG Q 1 " - " ASN C 233 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 943.8 milliseconds 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6230 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 40 sheets defined 23.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.767A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.141A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.129A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.695A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.509A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.030A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.586A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (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: 3.709A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.708A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.822A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.673A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.598A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.147A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.573A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.506A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1157 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.948A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.807A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.540A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.556A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.723A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.509A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.938A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.751A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.398A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.544A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.024A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 4.232A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.669A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 616 through 623 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.525A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.703A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 849 through 854 removed outlier: 4.127A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.631A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.807A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.814A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.750A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.869A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.859A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.463A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.313A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'C' and resid 1145 through 1161 removed outlier: 4.223A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.581A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 185 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 186 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.517A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.965A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.697A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.884A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.026A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.542A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.734A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 186 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.664A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.841A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A 132 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.424A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.540A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.800A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.185A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.189A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.617A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.199A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.239A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.338A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.502A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.941A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.531A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2493 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: 5.40 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8490 1.35 - 1.47: 7101 1.47 - 1.59: 11919 1.59 - 1.72: 0 1.72 - 1.84: 148 Bond restraints: 27658 Sorted by residual: bond pdb=" C LEU A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.12e-02 7.97e+03 3.64e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 27653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 36921 2.77 - 5.53: 581 5.53 - 8.30: 87 8.30 - 11.07: 17 11.07 - 13.83: 6 Bond angle restraints: 37612 Sorted by residual: angle pdb=" N PRO A 942 " pdb=" CA PRO A 942 " pdb=" CB PRO A 942 " ideal model delta sigma weight residual 101.83 110.19 -8.36 8.40e-01 1.42e+00 9.92e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 101.83 110.16 -8.33 8.40e-01 1.42e+00 9.84e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.36 110.26 -6.90 8.80e-01 1.29e+00 6.15e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.33 110.53 -7.20 9.30e-01 1.16e+00 6.00e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 111.77 103.78 7.99 1.04e+00 9.25e-01 5.91e+01 ... (remaining 37607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14209 17.89 - 35.77: 1435 35.77 - 53.66: 212 53.66 - 71.54: 39 71.54 - 89.43: 26 Dihedral angle restraints: 15921 sinusoidal: 6248 harmonic: 9673 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.50 -87.50 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.22 83.78 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA THR B1117 " pdb=" C THR B1117 " pdb=" N ASP B1118 " pdb=" CA ASP B1118 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 15918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4228 0.116 - 0.232: 189 0.232 - 0.347: 25 0.347 - 0.463: 2 0.463 - 0.579: 3 Chirality restraints: 4447 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 4444 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A1143 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 997 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ILE B 997 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 997 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 998 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 998 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR B 998 " 0.048 2.00e-02 2.50e+03 pdb=" O THR B 998 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 999 " -0.016 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4799 2.77 - 3.30: 25154 3.30 - 3.83: 43886 3.83 - 4.37: 47418 4.37 - 4.90: 81899 Nonbonded interactions: 203156 Sorted by model distance: nonbonded pdb=" OD1 ASN A 354 " pdb=" OG SER A 399 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.245 3.040 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.261 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.268 3.040 ... (remaining 203151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 702 or resid 704 through 1309)) selection = (chain 'B' and (resid 14 through 702 or resid 704 through 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 849 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.070 Find NCS groups from input model: 0.740 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.005 0.107 27765 Z= 0.247 Angle : 0.922 21.958 37885 Z= 0.467 Chirality : 0.059 0.579 4447 Planarity : 0.006 0.094 4756 Dihedral : 14.249 89.426 9574 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3283 helix: -0.18 (0.19), residues: 671 sheet: -0.17 (0.21), residues: 578 loop : -2.34 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 403 TYR 0.018 0.001 TYR C1067 PHE 0.027 0.001 PHE B 106 TRP 0.013 0.001 TRP C 633 HIS 0.017 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.25 (27658) covalent geometry : angle 0.87896 / 0.46 (37612) SS BOND : bond 0.00412 / 0.27 ( 39) SS BOND : angle 1.53064 / 0.97 ( 78) hydrogen bonds : bond 0.14200 / 9.57 ( 905) hydrogen bonds : angle 6.83706 / 4.62 ( 2493) Misc. bond : bond 0.00055 / 0.03 ( 3) link_BETA1-4 : bond 0.01064 / 0.76 ( 24) link_BETA1-4 : angle 2.83197 / 1.94 ( 72) link_NAG-ASN : bond 0.00970 / 0.65 ( 41) link_NAG-ASN : angle 4.41015 / 3.08 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: B 87 ASN cc_start: 0.4302 (OUTLIER) cc_final: 0.3625 (p0) REVERT: B 636 TYR cc_start: 0.5742 (t80) cc_final: 0.5472 (m-80) REVERT: A 167 TYR cc_start: 0.8242 (t80) cc_final: 0.7982 (t80) REVERT: C 613 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: C 896 ILE cc_start: 0.8178 (mm) cc_final: 0.7927 (tp) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.1364 time to fit residues: 34.8819 Evaluate side-chains 100 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 613 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.110450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085482 restraints weight = 118705.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.084495 restraints weight = 77511.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.085108 restraints weight = 60809.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085582 restraints weight = 53466.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085555 restraints weight = 49168.420| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27765 Z= 0.123 Angle : 0.652 18.337 37885 Z= 0.320 Chirality : 0.048 0.433 4447 Planarity : 0.004 0.084 4756 Dihedral : 5.147 39.111 3563 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.41 % Allowed : 6.85 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.63 (0.14), residues: 3283 helix: 0.66 (0.21), residues: 674 sheet: 0.02 (0.21), residues: 593 loop : -2.19 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.016 0.001 TYR C 269 PHE 0.020 0.001 PHE A 219 TRP 0.011 0.001 TRP C 633 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27658) covalent geometry : angle 0.61580 / 0.31 (37612) SS BOND : bond 0.00241 / 0.16 ( 39) SS BOND : angle 1.01645 / 0.67 ( 78) hydrogen bonds : bond 0.04483 / 3.08 ( 905) hydrogen bonds : angle 5.48189 / 3.72 ( 2493) Misc. bond : bond 0.00028 / 0.01 ( 3) link_BETA1-4 : bond 0.00734 / 0.45 ( 24) link_BETA1-4 : angle 1.89486 / 1.29 ( 72) link_NAG-ASN : bond 0.00707 / 0.47 ( 41) link_NAG-ASN : angle 3.50236 / 2.47 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 869 MET cc_start: 0.8584 (mtt) cc_final: 0.8320 (mtm) REVERT: B 964 LYS cc_start: 0.9076 (tppt) cc_final: 0.8766 (tppt) REVERT: A 731 MET cc_start: 0.8819 (ppp) cc_final: 0.8227 (ppp) REVERT: C 613 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7830 (pp30) REVERT: C 867 ASP cc_start: 0.7648 (p0) cc_final: 0.7406 (p0) REVERT: C 896 ILE cc_start: 0.8020 (mm) cc_final: 0.7812 (tp) REVERT: C 979 ASP cc_start: 0.7837 (t0) cc_final: 0.7435 (t0) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.1519 time to fit residues: 29.8032 Evaluate side-chains 107 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 121 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 316 optimal weight: 0.0070 chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 87 ASN B 185 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 536 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.106056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.080946 restraints weight = 119346.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079895 restraints weight = 75124.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080345 restraints weight = 68963.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080504 restraints weight = 60356.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080541 restraints weight = 54941.548| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27765 Z= 0.242 Angle : 0.750 17.931 37885 Z= 0.372 Chirality : 0.049 0.407 4447 Planarity : 0.005 0.082 4756 Dihedral : 5.480 36.986 3561 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.07 % Allowed : 13.12 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.73 (0.14), residues: 3283 helix: 0.66 (0.20), residues: 666 sheet: -0.27 (0.21), residues: 585 loop : -2.18 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 634 TYR 0.029 0.002 TYR C1067 PHE 0.033 0.002 PHE A 759 TRP 0.012 0.002 TRP C 633 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (27658) covalent geometry : angle 0.71393 / 0.36 (37612) SS BOND : bond 0.00379 / 0.25 ( 39) SS BOND : angle 1.17642 / 0.78 ( 78) hydrogen bonds : bond 0.05242 / 3.57 ( 905) hydrogen bonds : angle 5.69004 / 3.88 ( 2493) Misc. bond : bond 0.00039 / 0.02 ( 3) link_BETA1-4 : bond 0.00615 / 0.42 ( 24) link_BETA1-4 : angle 2.17961 / 1.49 ( 72) link_NAG-ASN : bond 0.00856 / 0.59 ( 41) link_NAG-ASN : angle 3.71420 / 2.62 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.040 Fit side-chains REVERT: A 511 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (t) REVERT: A 731 MET cc_start: 0.8705 (ppp) cc_final: 0.8263 (ppp) REVERT: A 882 ILE cc_start: 0.9216 (tp) cc_final: 0.9005 (mt) REVERT: C 128 ILE cc_start: 0.8947 (mm) cc_final: 0.8670 (tp) REVERT: C 583 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: C 613 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8016 (pp30) REVERT: C 867 ASP cc_start: 0.7804 (p0) cc_final: 0.7501 (p0) outliers start: 31 outliers final: 18 residues processed: 122 average time/residue: 0.1446 time to fit residues: 30.4348 Evaluate side-chains 112 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 132 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.107173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081957 restraints weight = 118642.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081329 restraints weight = 78429.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081732 restraints weight = 64229.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081978 restraints weight = 58718.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082008 restraints weight = 52625.000| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27765 Z= 0.155 Angle : 0.668 18.585 37885 Z= 0.327 Chirality : 0.048 0.398 4447 Planarity : 0.004 0.081 4756 Dihedral : 5.233 36.887 3561 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.45 % Allowed : 15.19 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.14), residues: 3283 helix: 0.96 (0.21), residues: 665 sheet: -0.34 (0.22), residues: 562 loop : -2.10 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE A 759 TRP 0.016 0.001 TRP B 64 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (27658) covalent geometry : angle 0.62665 / 0.32 (37612) SS BOND : bond 0.00271 / 0.19 ( 39) SS BOND : angle 1.34054 / 0.92 ( 78) hydrogen bonds : bond 0.04507 / 3.09 ( 905) hydrogen bonds : angle 5.43006 / 3.70 ( 2493) Misc. bond : bond 0.00036 / 0.02 ( 3) link_BETA1-4 : bond 0.00662 / 0.43 ( 24) link_BETA1-4 : angle 1.95597 / 1.31 ( 72) link_NAG-ASN : bond 0.00734 / 0.50 ( 41) link_NAG-ASN : angle 3.75560 / 2.82 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 1.091 Fit side-chains REVERT: B 1038 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8544 (tptt) REVERT: A 167 TYR cc_start: 0.7992 (t80) cc_final: 0.7755 (t80) REVERT: C 128 ILE cc_start: 0.8971 (mm) cc_final: 0.8691 (tp) REVERT: C 613 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7944 (pp30) REVERT: C 731 MET cc_start: 0.8463 (ppp) cc_final: 0.8262 (ppp) REVERT: C 867 ASP cc_start: 0.7830 (p0) cc_final: 0.7502 (p0) REVERT: C 994 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7986 (t70) REVERT: C 1145 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3638 (tp) outliers start: 42 outliers final: 23 residues processed: 134 average time/residue: 0.1370 time to fit residues: 32.5397 Evaluate side-chains 121 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 198 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.105574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080304 restraints weight = 118833.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079591 restraints weight = 78031.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079895 restraints weight = 66709.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080093 restraints weight = 60492.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080176 restraints weight = 54670.682| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27765 Z= 0.208 Angle : 0.713 18.268 37885 Z= 0.350 Chirality : 0.048 0.393 4447 Planarity : 0.004 0.080 4756 Dihedral : 5.388 37.685 3561 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.96 % Allowed : 16.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.73 (0.14), residues: 3283 helix: 0.79 (0.20), residues: 670 sheet: -0.50 (0.21), residues: 592 loop : -2.16 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.023 0.001 TYR C1067 PHE 0.027 0.002 PHE A 759 TRP 0.019 0.002 TRP B 64 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (27658) covalent geometry : angle 0.67488 / 0.34 (37612) SS BOND : bond 0.00308 / 0.21 ( 39) SS BOND : angle 1.25943 / 0.86 ( 78) hydrogen bonds : bond 0.04827 / 3.29 ( 905) hydrogen bonds : angle 5.56071 / 3.79 ( 2493) Misc. bond : bond 0.00039 / 0.02 ( 3) link_BETA1-4 : bond 0.00614 / 0.41 ( 24) link_BETA1-4 : angle 2.06177 / 1.38 ( 72) link_NAG-ASN : bond 0.00797 / 0.55 ( 41) link_NAG-ASN : angle 3.69931 / 2.64 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.8031 (t80) cc_final: 0.7798 (t80) REVERT: A 495 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.4745 (m-10) REVERT: A 511 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8273 (t) REVERT: A 731 MET cc_start: 0.8775 (ppp) cc_final: 0.8273 (ppp) REVERT: C 583 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 613 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8135 (pp30) REVERT: C 867 ASP cc_start: 0.7886 (p0) cc_final: 0.7543 (p0) REVERT: C 994 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8058 (t70) REVERT: C 1031 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 1145 LEU cc_start: 0.4382 (OUTLIER) cc_final: 0.3664 (tp) outliers start: 57 outliers final: 30 residues processed: 145 average time/residue: 0.1391 time to fit residues: 35.4225 Evaluate side-chains 127 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 30 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.0470 chunk 269 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.107817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083350 restraints weight = 118344.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081610 restraints weight = 83157.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.082183 restraints weight = 69336.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082777 restraints weight = 58317.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082712 restraints weight = 53545.388| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27765 Z= 0.117 Angle : 0.647 18.860 37885 Z= 0.315 Chirality : 0.047 0.414 4447 Planarity : 0.004 0.080 4756 Dihedral : 5.091 37.744 3561 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.58 % Allowed : 17.36 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.46 (0.15), residues: 3283 helix: 1.12 (0.21), residues: 670 sheet: -0.19 (0.22), residues: 550 loop : -2.05 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.012 0.001 TYR C 396 PHE 0.023 0.001 PHE A 219 TRP 0.019 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (27658) covalent geometry : angle 0.60967 / 0.31 (37612) SS BOND : bond 0.00243 / 0.17 ( 39) SS BOND : angle 1.27211 / 0.76 ( 78) hydrogen bonds : bond 0.04201 / 2.90 ( 905) hydrogen bonds : angle 5.26117 / 3.58 ( 2493) Misc. bond : bond 0.00031 / 0.02 ( 3) link_BETA1-4 : bond 0.00739 / 0.46 ( 24) link_BETA1-4 : angle 1.85895 / 1.24 ( 72) link_NAG-ASN : bond 0.00724 / 0.48 ( 41) link_NAG-ASN : angle 3.50965 / 2.49 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1030 SER cc_start: 0.9331 (m) cc_final: 0.8686 (t) REVERT: B 1038 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8625 (tptt) REVERT: A 461 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6204 (tp) REVERT: A 511 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (t) REVERT: A 731 MET cc_start: 0.8877 (ppp) cc_final: 0.8222 (ppp) REVERT: C 115 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.5863 (mp10) REVERT: C 128 ILE cc_start: 0.8854 (mm) cc_final: 0.8559 (tp) REVERT: C 583 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: C 613 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8001 (pp30) REVERT: C 731 MET cc_start: 0.8619 (ppp) cc_final: 0.8354 (ppp) REVERT: C 867 ASP cc_start: 0.7918 (p0) cc_final: 0.7558 (p0) REVERT: C 895 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7920 (pp30) REVERT: C 994 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8010 (t70) REVERT: C 1031 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7224 (mt-10) REVERT: C 1041 ASP cc_start: 0.7694 (t0) cc_final: 0.7341 (t0) outliers start: 46 outliers final: 20 residues processed: 142 average time/residue: 0.1315 time to fit residues: 32.9986 Evaluate side-chains 124 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 19 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 294 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.107066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081989 restraints weight = 118252.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.081471 restraints weight = 79536.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081785 restraints weight = 63925.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081968 restraints weight = 57468.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.082068 restraints weight = 51602.188| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27765 Z= 0.142 Angle : 0.655 19.154 37885 Z= 0.319 Chirality : 0.047 0.402 4447 Planarity : 0.004 0.079 4756 Dihedral : 5.094 38.375 3561 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.86 % Allowed : 17.53 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.50 (0.15), residues: 3283 helix: 1.04 (0.21), residues: 676 sheet: -0.19 (0.21), residues: 585 loop : -2.09 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.019 0.001 TYR A 167 PHE 0.022 0.001 PHE A 759 TRP 0.018 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27658) covalent geometry : angle 0.61709 / 0.31 (37612) SS BOND : bond 0.00309 / 0.22 ( 39) SS BOND : angle 1.27394 / 0.80 ( 78) hydrogen bonds : bond 0.04252 / 2.93 ( 905) hydrogen bonds : angle 5.27744 / 3.60 ( 2493) Misc. bond : bond 0.00040 / 0.02 ( 3) link_BETA1-4 : bond 0.00659 / 0.43 ( 24) link_BETA1-4 : angle 1.88364 / 1.26 ( 72) link_NAG-ASN : bond 0.00684 / 0.46 ( 41) link_NAG-ASN : angle 3.56325 / 2.53 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6127 (tp) REVERT: A 495 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.4586 (m-10) REVERT: A 511 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 731 MET cc_start: 0.8764 (ppp) cc_final: 0.8182 (ppp) REVERT: C 128 ILE cc_start: 0.8923 (mm) cc_final: 0.8546 (tp) REVERT: C 408 ARG cc_start: 0.7035 (ptp90) cc_final: 0.6778 (ptp90) REVERT: C 583 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: C 613 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: C 867 ASP cc_start: 0.7853 (p0) cc_final: 0.7506 (p0) REVERT: C 895 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7976 (pp30) REVERT: C 994 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7910 (t70) REVERT: C 1031 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7146 (mt-10) REVERT: C 1145 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3634 (tp) outliers start: 54 outliers final: 33 residues processed: 145 average time/residue: 0.1349 time to fit residues: 34.6589 Evaluate side-chains 135 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN 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 = 0.106281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081259 restraints weight = 119148.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080323 restraints weight = 78108.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080823 restraints weight = 65214.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081027 restraints weight = 58665.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081067 restraints weight = 53075.603| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27765 Z= 0.174 Angle : 0.682 19.266 37885 Z= 0.334 Chirality : 0.048 0.480 4447 Planarity : 0.004 0.079 4756 Dihedral : 5.185 38.675 3561 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.13 % Allowed : 17.80 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.58 (0.14), residues: 3283 helix: 0.96 (0.21), residues: 678 sheet: -0.28 (0.21), residues: 592 loop : -2.14 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE A 759 TRP 0.019 0.001 TRP B 64 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (27658) covalent geometry : angle 0.64342 / 0.33 (37612) SS BOND : bond 0.00309 / 0.22 ( 39) SS BOND : angle 1.37248 / 0.86 ( 78) hydrogen bonds : bond 0.04386 / 3.01 ( 905) hydrogen bonds : angle 5.34966 / 3.65 ( 2493) Misc. bond : bond 0.00029 / 0.02 ( 3) link_BETA1-4 : bond 0.00647 / 0.44 ( 24) link_BETA1-4 : angle 1.93242 / 1.29 ( 72) link_NAG-ASN : bond 0.00717 / 0.49 ( 41) link_NAG-ASN : angle 3.63231 / 2.59 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 97 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6120 (tp) REVERT: A 495 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.4624 (m-10) REVERT: A 511 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (t) REVERT: C 128 ILE cc_start: 0.8998 (mm) cc_final: 0.8661 (tp) REVERT: C 583 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: C 613 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8072 (pp30) REVERT: C 867 ASP cc_start: 0.7868 (p0) cc_final: 0.7526 (p0) REVERT: C 994 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8007 (t70) REVERT: C 1031 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 1145 LEU cc_start: 0.4359 (OUTLIER) cc_final: 0.3735 (tp) outliers start: 62 outliers final: 42 residues processed: 151 average time/residue: 0.1345 time to fit residues: 35.5578 Evaluate side-chains 141 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 326 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.106040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.081507 restraints weight = 118551.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079943 restraints weight = 82677.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080441 restraints weight = 70544.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080656 restraints weight = 61356.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080741 restraints weight = 55543.287| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27765 Z= 0.175 Angle : 0.692 19.373 37885 Z= 0.338 Chirality : 0.048 0.494 4447 Planarity : 0.004 0.078 4756 Dihedral : 5.243 39.183 3561 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.17 % Allowed : 17.94 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.62 (0.14), residues: 3283 helix: 0.96 (0.21), residues: 676 sheet: -0.30 (0.21), residues: 582 loop : -2.17 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.019 0.001 TYR C 396 PHE 0.028 0.001 PHE A 759 TRP 0.019 0.001 TRP B 64 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (27658) covalent geometry : angle 0.65447 / 0.33 (37612) SS BOND : bond 0.00307 / 0.21 ( 39) SS BOND : angle 1.26792 / 0.80 ( 78) hydrogen bonds : bond 0.04471 / 3.07 ( 905) hydrogen bonds : angle 5.39739 / 3.69 ( 2493) Misc. bond : bond 0.00032 / 0.02 ( 3) link_BETA1-4 : bond 0.00631 / 0.42 ( 24) link_BETA1-4 : angle 1.95379 / 1.30 ( 72) link_NAG-ASN : bond 0.00736 / 0.50 ( 41) link_NAG-ASN : angle 3.65558 / 2.60 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: B 774 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8524 (tp-100) REVERT: B 1030 SER cc_start: 0.9336 (m) cc_final: 0.8852 (t) REVERT: A 461 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6107 (tp) REVERT: A 495 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.4722 (m-10) REVERT: A 511 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8170 (t) REVERT: A 731 MET cc_start: 0.8913 (ppp) cc_final: 0.8325 (ppp) REVERT: C 128 ILE cc_start: 0.8962 (mm) cc_final: 0.8638 (tp) REVERT: C 583 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: C 613 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8210 (pp30) REVERT: C 867 ASP cc_start: 0.7959 (p0) cc_final: 0.7590 (p0) REVERT: C 994 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8199 (t70) REVERT: C 1031 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7601 (mt-10) REVERT: C 1041 ASP cc_start: 0.7915 (t0) cc_final: 0.7654 (t0) REVERT: C 1145 LEU cc_start: 0.4307 (OUTLIER) cc_final: 0.3746 (tp) outliers start: 63 outliers final: 45 residues processed: 151 average time/residue: 0.1303 time to fit residues: 35.0775 Evaluate side-chains 146 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 204 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 316 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 237 optimal weight: 0.0050 chunk 174 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 296 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080494 restraints weight = 118129.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079889 restraints weight = 78013.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080138 restraints weight = 65440.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.080461 restraints weight = 59594.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080493 restraints weight = 53842.857| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27765 Z= 0.184 Angle : 0.707 19.303 37885 Z= 0.345 Chirality : 0.048 0.460 4447 Planarity : 0.004 0.077 4756 Dihedral : 5.327 39.294 3561 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.03 % Allowed : 18.29 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.71 (0.14), residues: 3283 helix: 0.93 (0.21), residues: 670 sheet: -0.50 (0.20), residues: 616 loop : -2.21 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.020 0.001 TYR C 396 PHE 0.030 0.001 PHE A 759 TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (27658) covalent geometry : angle 0.66959 / 0.34 (37612) SS BOND : bond 0.00318 / 0.22 ( 39) SS BOND : angle 1.24102 / 0.78 ( 78) hydrogen bonds : bond 0.04566 / 3.12 ( 905) hydrogen bonds : angle 5.45883 / 3.73 ( 2493) Misc. bond : bond 0.00035 / 0.02 ( 3) link_BETA1-4 : bond 0.00608 / 0.40 ( 24) link_BETA1-4 : angle 1.99926 / 1.32 ( 72) link_NAG-ASN : bond 0.00750 / 0.51 ( 41) link_NAG-ASN : angle 3.70440 / 2.64 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 95 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 774 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8552 (tp-100) REVERT: B 1029 MET cc_start: 0.8912 (tpp) cc_final: 0.8667 (tpp) REVERT: B 1030 SER cc_start: 0.9305 (m) cc_final: 0.8832 (t) REVERT: A 495 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.4650 (m-10) REVERT: A 511 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8171 (t) REVERT: A 731 MET cc_start: 0.8808 (ppp) cc_final: 0.8214 (ppp) REVERT: C 128 ILE cc_start: 0.8982 (mm) cc_final: 0.8656 (tp) REVERT: C 583 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: C 613 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8226 (pp30) REVERT: C 867 ASP cc_start: 0.8043 (p0) cc_final: 0.7676 (p0) REVERT: C 994 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8219 (t70) REVERT: C 1031 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 1145 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.3914 (tp) outliers start: 59 outliers final: 46 residues processed: 147 average time/residue: 0.1346 time to fit residues: 34.8461 Evaluate side-chains 143 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 254 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 261 optimal weight: 0.2980 chunk 281 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.107410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082480 restraints weight = 117657.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081907 restraints weight = 77749.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082233 restraints weight = 62517.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082428 restraints weight = 57332.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082553 restraints weight = 52371.020| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27765 Z= 0.121 Angle : 0.659 19.693 37885 Z= 0.319 Chirality : 0.048 0.463 4447 Planarity : 0.004 0.079 4756 Dihedral : 5.077 38.422 3561 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.83 % Allowed : 18.63 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.47 (0.15), residues: 3283 helix: 1.25 (0.22), residues: 660 sheet: -0.20 (0.22), residues: 568 loop : -2.11 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.017 0.001 TYR A 167 PHE 0.019 0.001 PHE A 759 TRP 0.020 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27658) covalent geometry : angle 0.62226 / 0.31 (37612) SS BOND : bond 0.00256 / 0.18 ( 39) SS BOND : angle 1.10534 / 0.70 ( 78) hydrogen bonds : bond 0.04092 / 2.82 ( 905) hydrogen bonds : angle 5.22375 / 3.57 ( 2493) Misc. bond : bond 0.00019 / 0.01 ( 3) link_BETA1-4 : bond 0.00726 / 0.47 ( 24) link_BETA1-4 : angle 1.85475 / 1.23 ( 72) link_NAG-ASN : bond 0.00714 / 0.48 ( 41) link_NAG-ASN : angle 3.56542 / 2.54 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.47 seconds wall clock time: 60 minutes 50.98 seconds (3650.98 seconds total)