Starting phenix.real_space_refine on Thu Mar 5 16:22:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.map" model { file = "/net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ke6_22832/03_2026/7ke6_22832.cif" } resolution = 3.1 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= -0.001 sd= 0.055 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 99 5.16 5 C 15084 2.51 5 N 3852 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23688 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.97, per 1000 atoms: 0.25 Number of scatterers: 23688 At special positions: 0 Unit cell: (134.366, 129.076, 170.338, 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 99 16.00 O 4653 8.00 N 3852 7.00 C 15084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.07 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 343 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 122 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 27.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.311A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.720A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.702A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.731A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.753A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.612A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 4.025A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.243A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.459A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.699A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 4.228A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.359A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.530A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.619A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.628A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.536A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.759A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.789A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.882A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.319A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.543A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.292A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.979A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.208A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.287A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.514A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.528A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.726A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.833A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.783A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.507A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.580A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.604A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.507A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.527A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1140 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.135A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.603A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.523A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.249A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.175A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.175A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.798A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.510A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.752A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.923A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.923A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.280A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.662A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.426A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.294A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.891A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.227A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.095A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.095A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.902A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.442A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.316A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.121A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.229A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.710A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.017A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.814A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.988A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2790 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: 5.78 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6798 1.34 - 1.46: 4509 1.46 - 1.58: 12756 1.58 - 1.71: 0 1.71 - 1.83: 123 Bond restraints: 24186 Sorted by residual: bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 24181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 29147 2.81 - 5.62: 3650 5.62 - 8.43: 82 8.43 - 11.24: 4 11.24 - 14.06: 3 Bond angle restraints: 32886 Sorted by residual: angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 120.14 -11.07 1.52e+00 4.33e-01 5.30e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 119.72 -10.76 1.49e+00 4.50e-01 5.21e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 128.46 -14.06 2.30e+00 1.89e-01 3.73e+01 angle pdb=" C CYS B 166 " pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 120.28 128.41 -8.13 1.34e+00 5.57e-01 3.68e+01 angle pdb=" C CYS B 166 " pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sigma weight residual 110.42 122.33 -11.91 1.99e+00 2.53e-01 3.58e+01 ... (remaining 32881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14113 17.90 - 35.79: 859 35.79 - 53.69: 140 53.69 - 71.58: 57 71.58 - 89.48: 44 Dihedral angle restraints: 15213 sinusoidal: 6729 harmonic: 8484 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.18 80.18 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.02 80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.51 79.51 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2898 0.111 - 0.222: 949 0.222 - 0.333: 91 0.333 - 0.444: 8 0.444 - 0.555: 2 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.95e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.35e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.85e+01 ... (remaining 3945 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.225 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" CG ASN B 331 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.465 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " -0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.195 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" CG ASN A 331 " 0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.341 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.161 2.00e-02 2.50e+03 1.75e-01 3.83e+02 pdb=" CG ASN B1074 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.273 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.210 2.00e-02 2.50e+03 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 12860 3.03 - 3.49: 22428 3.49 - 3.96: 38729 3.96 - 4.43: 42785 4.43 - 4.90: 72188 Nonbonded interactions: 188990 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.558 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.564 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.566 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.569 3.040 ... (remaining 188985 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.190 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.086 24285 Z= 0.772 Angle : 1.790 14.056 33147 Z= 1.174 Chirality : 0.099 0.555 3948 Planarity : 0.013 0.150 4155 Dihedral : 13.181 89.476 9627 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.47 % Favored : 93.25 % Rotamer: Outliers : 1.02 % Allowed : 3.21 % Favored : 95.77 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 2844 helix: -1.34 (0.16), residues: 657 sheet: 0.12 (0.20), residues: 583 loop : -1.15 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 190 TYR 0.143 0.019 TYR A 269 PHE 0.075 0.012 PHE B 802 TRP 0.101 0.024 TRP A 886 HIS 0.011 0.003 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.01369 (24186) covalent geometry : angle 1.76173 (32886) SS BOND : bond 0.01352 ( 36) SS BOND : angle 2.18708 ( 72) hydrogen bonds : bond 0.16559 ( 999) hydrogen bonds : angle 8.78565 ( 2790) link_BETA1-4 : bond 0.02460 ( 15) link_BETA1-4 : angle 4.24648 ( 45) link_NAG-ASN : bond 0.02387 ( 48) link_NAG-ASN : angle 4.55780 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.7875 (t80) cc_final: 0.7473 (t80) REVERT: B 976 VAL cc_start: 0.8692 (t) cc_final: 0.8465 (t) REVERT: B 1004 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (tt) REVERT: C 523 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.6207 (p) REVERT: C 1004 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 26 outliers final: 6 residues processed: 344 average time/residue: 0.1916 time to fit residues: 99.0306 Evaluate side-chains 159 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1002 GLN B 207 HIS B 317 ASN B 422 ASN B 907 ASN C 207 HIS C 907 ASN C 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083868 restraints weight = 40518.809| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.44 r_work: 0.3030 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24285 Z= 0.158 Angle : 0.744 15.721 33147 Z= 0.371 Chirality : 0.050 1.038 3948 Planarity : 0.004 0.034 4155 Dihedral : 6.383 59.253 4438 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.61 % Allowed : 7.13 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2844 helix: 0.59 (0.20), residues: 659 sheet: -0.15 (0.18), residues: 712 loop : -0.79 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.019 0.002 TYR B1067 PHE 0.018 0.002 PHE A 220 TRP 0.023 0.003 TRP C 64 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (24186) covalent geometry : angle 0.68265 (32886) SS BOND : bond 0.00525 ( 36) SS BOND : angle 2.03341 ( 72) hydrogen bonds : bond 0.04521 ( 999) hydrogen bonds : angle 6.42921 ( 2790) link_BETA1-4 : bond 0.00526 ( 15) link_BETA1-4 : angle 1.77454 ( 45) link_NAG-ASN : bond 0.00546 ( 48) link_NAG-ASN : angle 4.24308 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8063 (m-80) cc_final: 0.6714 (m-80) REVERT: A 408 ARG cc_start: 0.8644 (tmm160) cc_final: 0.8423 (ppt170) REVERT: A 531 THR cc_start: 0.8707 (t) cc_final: 0.8234 (p) REVERT: A 571 ASP cc_start: 0.7807 (t0) cc_final: 0.7332 (t0) REVERT: A 762 GLN cc_start: 0.8393 (pt0) cc_final: 0.8070 (pt0) REVERT: A 1119 ASN cc_start: 0.8232 (m-40) cc_final: 0.7999 (m110) REVERT: B 309 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 347 PHE cc_start: 0.7105 (m-10) cc_final: 0.6635 (m-10) REVERT: B 380 TYR cc_start: 0.7670 (m-80) cc_final: 0.7007 (m-80) REVERT: B 427 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: B 434 ILE cc_start: 0.7897 (mt) cc_final: 0.7625 (mm) REVERT: B 603 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8577 (t0) REVERT: B 988 GLU cc_start: 0.7408 (mp0) cc_final: 0.7068 (mp0) REVERT: C 220 PHE cc_start: 0.6664 (t80) cc_final: 0.6459 (t80) REVERT: C 229 LEU cc_start: 0.8454 (mp) cc_final: 0.7331 (tt) REVERT: C 565 PHE cc_start: 0.6240 (m-80) cc_final: 0.5963 (m-80) REVERT: C 571 ASP cc_start: 0.7317 (t0) cc_final: 0.6877 (t0) REVERT: C 737 ASP cc_start: 0.8012 (t0) cc_final: 0.7809 (t0) REVERT: C 855 PHE cc_start: 0.8288 (m-10) cc_final: 0.7886 (m-80) REVERT: C 1004 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8339 (tt) outliers start: 41 outliers final: 18 residues processed: 209 average time/residue: 0.1653 time to fit residues: 54.4555 Evaluate side-chains 153 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 151 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 955 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081138 restraints weight = 40728.815| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.36 r_work: 0.2960 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24285 Z= 0.232 Angle : 0.683 16.460 33147 Z= 0.342 Chirality : 0.048 0.692 3948 Planarity : 0.004 0.037 4155 Dihedral : 5.750 55.408 4431 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.49 % Allowed : 9.28 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 2844 helix: 0.96 (0.20), residues: 662 sheet: -0.10 (0.18), residues: 685 loop : -0.74 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.025 0.002 TYR B 265 PHE 0.032 0.002 PHE B 400 TRP 0.028 0.003 TRP B 353 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00555 (24186) covalent geometry : angle 0.63965 (32886) SS BOND : bond 0.00456 ( 36) SS BOND : angle 1.70915 ( 72) hydrogen bonds : bond 0.04360 ( 999) hydrogen bonds : angle 6.07468 ( 2790) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.46286 ( 45) link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 3.41467 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8693 (mpp80) cc_final: 0.8196 (mpp80) REVERT: A 408 ARG cc_start: 0.8703 (tmm160) cc_final: 0.8412 (tmm-80) REVERT: A 531 THR cc_start: 0.8819 (t) cc_final: 0.8362 (p) REVERT: A 571 ASP cc_start: 0.7898 (t0) cc_final: 0.7282 (t0) REVERT: A 762 GLN cc_start: 0.8461 (pt0) cc_final: 0.8188 (pt0) REVERT: A 804 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8370 (mm110) REVERT: A 902 MET cc_start: 0.8625 (mmt) cc_final: 0.8391 (mmt) REVERT: A 950 ASP cc_start: 0.8635 (t70) cc_final: 0.8384 (p0) REVERT: B 104 TRP cc_start: 0.8121 (m-90) cc_final: 0.7844 (m-90) REVERT: B 380 TYR cc_start: 0.7866 (m-80) cc_final: 0.7202 (m-80) REVERT: B 451 TYR cc_start: 0.6897 (m-10) cc_final: 0.6551 (m-10) REVERT: B 603 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (t0) REVERT: B 1050 MET cc_start: 0.8030 (ptt) cc_final: 0.7654 (ptm) REVERT: C 141 LEU cc_start: 0.7546 (tp) cc_final: 0.7137 (pp) REVERT: C 220 PHE cc_start: 0.6835 (t80) cc_final: 0.6568 (t80) REVERT: C 737 ASP cc_start: 0.8088 (t0) cc_final: 0.7835 (t0) REVERT: C 786 LYS cc_start: 0.8498 (pttt) cc_final: 0.8001 (mmmt) REVERT: C 855 PHE cc_start: 0.8424 (m-10) cc_final: 0.8072 (m-80) REVERT: C 988 GLU cc_start: 0.8482 (mp0) cc_final: 0.8194 (mp0) REVERT: C 1004 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 38 outliers final: 16 residues processed: 172 average time/residue: 0.1533 time to fit residues: 42.0295 Evaluate side-chains 138 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.127515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082399 restraints weight = 40373.199| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.37 r_work: 0.2974 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24285 Z= 0.159 Angle : 0.605 13.887 33147 Z= 0.303 Chirality : 0.046 0.525 3948 Planarity : 0.004 0.042 4155 Dihedral : 5.363 54.372 4429 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.76 % Allowed : 9.67 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2844 helix: 1.32 (0.21), residues: 658 sheet: -0.03 (0.18), residues: 668 loop : -0.68 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.021 0.001 TYR B1067 PHE 0.024 0.001 PHE B 400 TRP 0.027 0.002 TRP A 104 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00373 (24186) covalent geometry : angle 0.56376 (32886) SS BOND : bond 0.00468 ( 36) SS BOND : angle 2.05345 ( 72) hydrogen bonds : bond 0.03791 ( 999) hydrogen bonds : angle 5.81116 ( 2790) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 1.23400 ( 45) link_NAG-ASN : bond 0.00332 ( 48) link_NAG-ASN : angle 3.00634 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.8494 (t) cc_final: 0.8208 (m) REVERT: A 224 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: A 340 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8586 (mp0) REVERT: A 408 ARG cc_start: 0.8727 (tmm160) cc_final: 0.8065 (tmm-80) REVERT: A 414 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: A 531 THR cc_start: 0.8788 (t) cc_final: 0.8352 (p) REVERT: A 571 ASP cc_start: 0.7918 (t0) cc_final: 0.7312 (t0) REVERT: A 762 GLN cc_start: 0.8376 (pt0) cc_final: 0.8056 (pt0) REVERT: A 950 ASP cc_start: 0.8607 (t70) cc_final: 0.8079 (m-30) REVERT: B 104 TRP cc_start: 0.8069 (m-90) cc_final: 0.7756 (m-90) REVERT: B 346 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.6993 (mmp-170) REVERT: B 378 LYS cc_start: 0.8561 (mttp) cc_final: 0.8217 (ptpp) REVERT: B 380 TYR cc_start: 0.7752 (m-80) cc_final: 0.7248 (m-80) REVERT: B 434 ILE cc_start: 0.8035 (mm) cc_final: 0.7695 (mm) REVERT: B 603 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 220 PHE cc_start: 0.6576 (t80) cc_final: 0.6295 (t80) REVERT: C 697 MET cc_start: 0.8563 (ptp) cc_final: 0.8322 (ptm) REVERT: C 988 GLU cc_start: 0.8508 (mp0) cc_final: 0.8248 (mp0) REVERT: C 1004 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 45 outliers final: 22 residues processed: 170 average time/residue: 0.1499 time to fit residues: 41.9161 Evaluate side-chains 143 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 220 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.081067 restraints weight = 40173.803| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.35 r_work: 0.3031 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24285 Z= 0.147 Angle : 0.581 13.564 33147 Z= 0.289 Chirality : 0.045 0.459 3948 Planarity : 0.003 0.042 4155 Dihedral : 5.178 54.227 4429 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.15 % Allowed : 9.71 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2844 helix: 1.58 (0.21), residues: 656 sheet: 0.07 (0.19), residues: 657 loop : -0.63 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.021 0.001 TYR B1067 PHE 0.022 0.001 PHE B 400 TRP 0.022 0.002 TRP B 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (24186) covalent geometry : angle 0.54321 (32886) SS BOND : bond 0.00433 ( 36) SS BOND : angle 1.58072 ( 72) hydrogen bonds : bond 0.03609 ( 999) hydrogen bonds : angle 5.63698 ( 2790) link_BETA1-4 : bond 0.00433 ( 15) link_BETA1-4 : angle 1.17954 ( 45) link_NAG-ASN : bond 0.00304 ( 48) link_NAG-ASN : angle 2.93568 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.8399 (t) cc_final: 0.8106 (m) REVERT: A 224 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: A 269 TYR cc_start: 0.8216 (m-80) cc_final: 0.7793 (m-80) REVERT: A 340 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8588 (mp0) REVERT: A 408 ARG cc_start: 0.8724 (tmm160) cc_final: 0.8076 (tmm-80) REVERT: A 414 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7878 (tp-100) REVERT: A 531 THR cc_start: 0.8811 (t) cc_final: 0.8399 (p) REVERT: A 571 ASP cc_start: 0.7920 (t0) cc_final: 0.7292 (t0) REVERT: A 762 GLN cc_start: 0.8350 (pt0) cc_final: 0.8059 (pt0) REVERT: A 950 ASP cc_start: 0.8565 (t70) cc_final: 0.8056 (m-30) REVERT: B 104 TRP cc_start: 0.8062 (m-90) cc_final: 0.7747 (m-90) REVERT: B 346 ARG cc_start: 0.7319 (tpp-160) cc_final: 0.7106 (mmp80) REVERT: B 378 LYS cc_start: 0.8597 (mttp) cc_final: 0.8251 (ptpp) REVERT: B 380 TYR cc_start: 0.7720 (m-80) cc_final: 0.7260 (m-80) REVERT: B 389 ASP cc_start: 0.8216 (t0) cc_final: 0.7852 (t0) REVERT: B 434 ILE cc_start: 0.8013 (mm) cc_final: 0.7773 (mm) REVERT: B 558 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8829 (mmtm) REVERT: B 603 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (t0) REVERT: C 220 PHE cc_start: 0.6579 (t80) cc_final: 0.6244 (t80) REVERT: C 697 MET cc_start: 0.8586 (ptp) cc_final: 0.8307 (ptm) REVERT: C 977 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 988 GLU cc_start: 0.8529 (mp0) cc_final: 0.8289 (mp0) REVERT: C 1004 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8301 (tt) outliers start: 55 outliers final: 27 residues processed: 177 average time/residue: 0.1474 time to fit residues: 43.0872 Evaluate side-chains 153 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 147 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1071 GLN C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.129781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085793 restraints weight = 39956.444| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.30 r_work: 0.2981 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24285 Z= 0.122 Angle : 0.557 12.339 33147 Z= 0.277 Chirality : 0.044 0.415 3948 Planarity : 0.003 0.042 4155 Dihedral : 4.905 53.859 4429 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 10.30 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 2844 helix: 1.68 (0.21), residues: 660 sheet: 0.12 (0.19), residues: 676 loop : -0.62 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.020 0.001 TYR B1067 PHE 0.021 0.001 PHE B 400 TRP 0.020 0.002 TRP B 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00279 (24186) covalent geometry : angle 0.52441 (32886) SS BOND : bond 0.00429 ( 36) SS BOND : angle 1.70690 ( 72) hydrogen bonds : bond 0.03419 ( 999) hydrogen bonds : angle 5.49280 ( 2790) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.09789 ( 45) link_NAG-ASN : bond 0.00323 ( 48) link_NAG-ASN : angle 2.62103 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8723 (p) cc_final: 0.8447 (t) REVERT: A 221 SER cc_start: 0.8357 (t) cc_final: 0.8088 (m) REVERT: A 224 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5579 (pm20) REVERT: A 269 TYR cc_start: 0.8270 (m-80) cc_final: 0.7946 (m-80) REVERT: A 340 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8591 (mp0) REVERT: A 408 ARG cc_start: 0.8770 (tmm160) cc_final: 0.8127 (tmm-80) REVERT: A 414 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7878 (tp-100) REVERT: A 531 THR cc_start: 0.8805 (t) cc_final: 0.8404 (p) REVERT: A 571 ASP cc_start: 0.7980 (t0) cc_final: 0.7357 (t0) REVERT: A 762 GLN cc_start: 0.8310 (pt0) cc_final: 0.7985 (pt0) REVERT: A 950 ASP cc_start: 0.8542 (t70) cc_final: 0.8029 (m-30) REVERT: B 96 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8151 (mp0) REVERT: B 104 TRP cc_start: 0.7992 (m-90) cc_final: 0.7659 (m-90) REVERT: B 389 ASP cc_start: 0.8173 (t0) cc_final: 0.7830 (t0) REVERT: B 414 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6987 (mp10) REVERT: B 434 ILE cc_start: 0.7953 (mm) cc_final: 0.7713 (mm) REVERT: B 603 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8461 (t0) REVERT: B 1050 MET cc_start: 0.7949 (ptt) cc_final: 0.7687 (ptm) REVERT: C 220 PHE cc_start: 0.6472 (t80) cc_final: 0.6134 (t80) REVERT: C 977 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8124 (tt) REVERT: C 988 GLU cc_start: 0.8564 (mp0) cc_final: 0.8309 (mp0) REVERT: C 1004 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8348 (tt) outliers start: 51 outliers final: 31 residues processed: 185 average time/residue: 0.1543 time to fit residues: 47.0561 Evaluate side-chains 165 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 137 optimal weight: 0.0060 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081628 restraints weight = 40231.578| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.34 r_work: 0.3040 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24285 Z= 0.133 Angle : 0.551 12.385 33147 Z= 0.274 Chirality : 0.044 0.393 3948 Planarity : 0.003 0.042 4155 Dihedral : 4.929 54.287 4429 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.72 % Allowed : 11.12 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2844 helix: 1.73 (0.21), residues: 660 sheet: 0.14 (0.19), residues: 675 loop : -0.60 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE B 400 TRP 0.023 0.002 TRP B 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00310 (24186) covalent geometry : angle 0.52171 (32886) SS BOND : bond 0.00424 ( 36) SS BOND : angle 1.37067 ( 72) hydrogen bonds : bond 0.03414 ( 999) hydrogen bonds : angle 5.41424 ( 2790) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 1.08405 ( 45) link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 2.54915 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8718 (p) cc_final: 0.8451 (t) REVERT: A 221 SER cc_start: 0.8345 (t) cc_final: 0.8084 (m) REVERT: A 224 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5607 (pm20) REVERT: A 340 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8569 (mp0) REVERT: A 408 ARG cc_start: 0.8763 (tmm160) cc_final: 0.8095 (tmm-80) REVERT: A 414 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (tp-100) REVERT: A 531 THR cc_start: 0.8827 (t) cc_final: 0.8432 (p) REVERT: A 571 ASP cc_start: 0.7983 (t0) cc_final: 0.7358 (t0) REVERT: A 762 GLN cc_start: 0.8304 (pt0) cc_final: 0.7992 (pt0) REVERT: A 950 ASP cc_start: 0.8535 (t70) cc_final: 0.8030 (m-30) REVERT: B 96 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8150 (mp0) REVERT: B 104 TRP cc_start: 0.7990 (m-90) cc_final: 0.7673 (m-90) REVERT: B 389 ASP cc_start: 0.8142 (t0) cc_final: 0.7808 (t0) REVERT: B 428 ASP cc_start: 0.8925 (t0) cc_final: 0.8623 (t0) REVERT: B 434 ILE cc_start: 0.7973 (mm) cc_final: 0.7719 (mm) REVERT: B 516 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6969 (mt-10) REVERT: B 603 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8448 (t0) REVERT: C 220 PHE cc_start: 0.6538 (t80) cc_final: 0.6181 (t80) REVERT: C 902 MET cc_start: 0.8335 (mmt) cc_final: 0.8131 (mmt) REVERT: C 977 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8129 (tt) REVERT: C 988 GLU cc_start: 0.8557 (mp0) cc_final: 0.8282 (mp0) REVERT: C 1004 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8331 (tt) outliers start: 44 outliers final: 33 residues processed: 174 average time/residue: 0.1563 time to fit residues: 44.8042 Evaluate side-chains 169 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 290 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076413 restraints weight = 40792.223| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.35 r_work: 0.2946 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 24285 Z= 0.352 Angle : 0.708 13.133 33147 Z= 0.353 Chirality : 0.049 0.349 3948 Planarity : 0.004 0.041 4155 Dihedral : 5.434 56.039 4429 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.84 % Allowed : 11.01 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 2844 helix: 1.21 (0.20), residues: 671 sheet: -0.07 (0.19), residues: 671 loop : -0.84 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 905 TYR 0.031 0.002 TYR B 265 PHE 0.031 0.002 PHE B1121 TRP 0.018 0.002 TRP B 353 HIS 0.014 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00841 (24186) covalent geometry : angle 0.68046 (32886) SS BOND : bond 0.00513 ( 36) SS BOND : angle 1.71149 ( 72) hydrogen bonds : bond 0.04385 ( 999) hydrogen bonds : angle 5.90742 ( 2790) link_BETA1-4 : bond 0.00231 ( 15) link_BETA1-4 : angle 1.18252 ( 45) link_NAG-ASN : bond 0.00408 ( 48) link_NAG-ASN : angle 2.80299 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8574 (p) cc_final: 0.8299 (t) REVERT: A 224 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5938 (pm20) REVERT: A 408 ARG cc_start: 0.8774 (tmm160) cc_final: 0.8370 (tmm-80) REVERT: A 465 GLU cc_start: 0.5460 (pt0) cc_final: 0.5242 (pt0) REVERT: A 571 ASP cc_start: 0.8134 (t0) cc_final: 0.7491 (t0) REVERT: A 697 MET cc_start: 0.8816 (ptm) cc_final: 0.8599 (ptp) REVERT: A 950 ASP cc_start: 0.8652 (t70) cc_final: 0.8436 (p0) REVERT: B 96 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8349 (mp0) REVERT: B 389 ASP cc_start: 0.8314 (t0) cc_final: 0.8028 (t0) REVERT: B 428 ASP cc_start: 0.8921 (t0) cc_final: 0.8608 (t0) REVERT: B 434 ILE cc_start: 0.8164 (mm) cc_final: 0.7857 (mm) REVERT: B 516 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7027 (mt-10) REVERT: B 979 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7919 (t0) REVERT: C 977 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8280 (tt) REVERT: C 988 GLU cc_start: 0.8556 (mp0) cc_final: 0.8189 (mp0) REVERT: C 994 ASP cc_start: 0.8954 (t0) cc_final: 0.8716 (t0) REVERT: C 1004 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 47 outliers final: 30 residues processed: 164 average time/residue: 0.1575 time to fit residues: 41.8083 Evaluate side-chains 158 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 0.5980 chunk 112 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079757 restraints weight = 40691.187| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.34 r_work: 0.2938 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 24285 Z= 0.154 Angle : 0.584 13.430 33147 Z= 0.292 Chirality : 0.045 0.367 3948 Planarity : 0.003 0.043 4155 Dihedral : 5.125 56.999 4429 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.65 % Allowed : 11.56 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2844 helix: 1.60 (0.21), residues: 665 sheet: -0.05 (0.19), residues: 675 loop : -0.74 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.021 0.001 TYR B1067 PHE 0.019 0.001 PHE B 400 TRP 0.024 0.002 TRP B 104 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00361 (24186) covalent geometry : angle 0.55257 (32886) SS BOND : bond 0.00510 ( 36) SS BOND : angle 1.93964 ( 72) hydrogen bonds : bond 0.03662 ( 999) hydrogen bonds : angle 5.61322 ( 2790) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.04731 ( 45) link_NAG-ASN : bond 0.00318 ( 48) link_NAG-ASN : angle 2.54078 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8553 (p) cc_final: 0.8266 (t) REVERT: A 224 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5598 (pm20) REVERT: A 340 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8633 (mp0) REVERT: A 408 ARG cc_start: 0.8740 (tmm160) cc_final: 0.8017 (tmm-80) REVERT: A 414 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7827 (tp-100) REVERT: A 531 THR cc_start: 0.8834 (t) cc_final: 0.8427 (p) REVERT: A 571 ASP cc_start: 0.7996 (t0) cc_final: 0.7432 (t0) REVERT: A 762 GLN cc_start: 0.8386 (pt0) cc_final: 0.8051 (pt0) REVERT: A 950 ASP cc_start: 0.8580 (t70) cc_final: 0.8091 (m-30) REVERT: A 1132 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8998 (tt) REVERT: B 96 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8313 (mp0) REVERT: B 389 ASP cc_start: 0.8259 (t0) cc_final: 0.7978 (t0) REVERT: B 428 ASP cc_start: 0.8905 (t0) cc_final: 0.8375 (p0) REVERT: B 434 ILE cc_start: 0.8075 (mm) cc_final: 0.7771 (mm) REVERT: B 516 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6911 (mt-10) REVERT: C 200 TYR cc_start: 0.7052 (m-80) cc_final: 0.5723 (m-80) REVERT: C 319 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7949 (mtt-85) REVERT: C 977 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 988 GLU cc_start: 0.8536 (mp0) cc_final: 0.8237 (mp0) REVERT: C 994 ASP cc_start: 0.8940 (t0) cc_final: 0.8702 (t0) REVERT: C 1004 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 42 outliers final: 31 residues processed: 168 average time/residue: 0.1626 time to fit residues: 44.2358 Evaluate side-chains 167 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 166 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.125118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079852 restraints weight = 40412.655| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.34 r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24285 Z= 0.161 Angle : 0.581 13.688 33147 Z= 0.288 Chirality : 0.045 0.345 3948 Planarity : 0.003 0.043 4155 Dihedral : 4.994 59.368 4429 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.45 % Allowed : 11.79 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2844 helix: 1.66 (0.21), residues: 673 sheet: -0.01 (0.19), residues: 672 loop : -0.69 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE B 400 TRP 0.036 0.002 TRP B 104 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00381 (24186) covalent geometry : angle 0.55352 (32886) SS BOND : bond 0.00410 ( 36) SS BOND : angle 1.73102 ( 72) hydrogen bonds : bond 0.03598 ( 999) hydrogen bonds : angle 5.53868 ( 2790) link_BETA1-4 : bond 0.00284 ( 15) link_BETA1-4 : angle 1.02399 ( 45) link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 2.44452 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8580 (p) cc_final: 0.8305 (t) REVERT: A 62 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 224 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5694 (pm20) REVERT: A 340 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8645 (mp0) REVERT: A 408 ARG cc_start: 0.8749 (tmm160) cc_final: 0.8226 (tmm-80) REVERT: A 414 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: A 531 THR cc_start: 0.8814 (t) cc_final: 0.8417 (p) REVERT: A 571 ASP cc_start: 0.8027 (t0) cc_final: 0.7458 (t0) REVERT: A 1132 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 96 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8297 (mp0) REVERT: B 389 ASP cc_start: 0.8255 (t0) cc_final: 0.7965 (t0) REVERT: B 428 ASP cc_start: 0.8877 (t0) cc_final: 0.8341 (p0) REVERT: B 434 ILE cc_start: 0.8081 (mm) cc_final: 0.7836 (mm) REVERT: B 516 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6893 (mt-10) REVERT: C 200 TYR cc_start: 0.6793 (m-80) cc_final: 0.5571 (m-80) REVERT: C 319 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7977 (mtt-85) REVERT: C 577 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6404 (ttm170) REVERT: C 977 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (tt) REVERT: C 988 GLU cc_start: 0.8534 (mp0) cc_final: 0.8221 (mp0) REVERT: C 1004 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8328 (tt) outliers start: 37 outliers final: 31 residues processed: 165 average time/residue: 0.1619 time to fit residues: 42.9565 Evaluate side-chains 168 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 218 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080017 restraints weight = 40328.813| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.33 r_work: 0.2939 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 24285 Z= 0.168 Angle : 0.721 59.184 33147 Z= 0.387 Chirality : 0.045 0.509 3948 Planarity : 0.003 0.043 4155 Dihedral : 4.991 59.352 4429 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.65 % Allowed : 11.71 % Favored : 86.64 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2844 helix: 1.68 (0.21), residues: 673 sheet: -0.01 (0.19), residues: 672 loop : -0.69 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.020 0.001 TYR B1067 PHE 0.015 0.001 PHE B 400 TRP 0.032 0.002 TRP B 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (24186) covalent geometry : angle 0.69973 (32886) SS BOND : bond 0.00403 ( 36) SS BOND : angle 1.67050 ( 72) hydrogen bonds : bond 0.03584 ( 999) hydrogen bonds : angle 5.53918 ( 2790) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 1.03306 ( 45) link_NAG-ASN : bond 0.00309 ( 48) link_NAG-ASN : angle 2.44535 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.61 seconds wall clock time: 95 minutes 35.03 seconds (5735.03 seconds total)