Starting phenix.real_space_refine on Thu Mar 5 19:38:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toy_26041/03_2026/7toy_26041.map" } resolution = 3.53 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= -0.004 sd= 0.138 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 105 5.16 5 C 15697 2.51 5 N 4036 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 24673 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7910 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 7 Chain: "B" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7924 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 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: "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: 5.78, per 1000 atoms: 0.23 Number of scatterers: 24673 At special positions: 0 Unit cell: (133.92, 137.16, 176.04, 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 105 16.00 O 4835 8.00 N 4036 7.00 C 15697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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-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 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " 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 B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5714 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 46 sheets defined 27.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.054A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.207A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.506A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.816A 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: 4.218A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.568A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.736A 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: 3.725A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.579A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.566A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.620A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.911A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.560A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.124A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.965A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.502A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.987A 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 816 through 826 removed outlier: 3.650A 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: 3.685A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.673A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.820A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.721A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.866A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.251A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 removed outlier: 3.917A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 626 through 629' Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.932A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.754A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.637A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.591A 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: 3.696A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.863A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.493A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.897A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.317A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.039A 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: 3.942A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.516A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.104A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.644A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.093A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.581A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.093A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.997A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.970A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.941A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.679A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 removed outlier: 6.632A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.541A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.908A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.829A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.114A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.559A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.894A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.508A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.719A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.307A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.665A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.761A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.490A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.490A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.944A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 3.01 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: 7431 1.34 - 1.46: 4716 1.46 - 1.59: 12932 1.59 - 1.71: 0 1.71 - 1.84: 129 Bond restraints: 25208 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.495 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.494 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.493 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 25203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 33803 4.46 - 8.91: 482 8.91 - 13.37: 7 13.37 - 17.82: 0 17.82 - 22.28: 1 Bond angle restraints: 34293 Sorted by residual: angle pdb=" CA VAL A 635 " pdb=" CB VAL A 635 " pdb=" CG1 VAL A 635 " ideal model delta sigma weight residual 110.40 132.68 -22.28 1.70e+00 3.46e-01 1.72e+02 angle pdb=" N ARG B 454 " pdb=" CA ARG B 454 " pdb=" C ARG B 454 " ideal model delta sigma weight residual 111.40 120.06 -8.66 1.22e+00 6.72e-01 5.03e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.54 -10.47 1.52e+00 4.33e-01 4.75e+01 angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 108.79 118.80 -10.01 1.53e+00 4.27e-01 4.28e+01 angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.25 6.35 1.00e+00 1.00e+00 4.03e+01 ... (remaining 34288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14686 17.99 - 35.99: 874 35.99 - 53.98: 157 53.98 - 71.97: 52 71.97 - 89.97: 36 Dihedral angle restraints: 15805 sinusoidal: 6933 harmonic: 8872 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.93 82.93 1 1.00e+01 1.00e-02 8.42e+01 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 -143.09 57.09 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" C ARG C 457 " pdb=" N ARG C 457 " pdb=" CA ARG C 457 " pdb=" CB ARG C 457 " ideal model delta harmonic sigma weight residual -122.60 -138.26 15.66 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 15802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4070 0.305 - 0.610: 15 0.610 - 0.914: 0 0.914 - 1.219: 0 1.219 - 1.524: 1 Chirality restraints: 4086 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.53e+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 -2.59 0.19 2.00e-02 2.50e+03 9.45e+01 ... (remaining 4083 not shown) Planarity restraints: 4400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.141 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" CG ASN B 657 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.137 2.00e-02 2.50e+03 1.45e-01 2.64e+02 pdb=" CG ASN C 616 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.135 2.00e-02 2.50e+03 1.42e-01 2.51e+02 pdb=" CG ASN A 165 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.214 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.169 2.00e-02 2.50e+03 ... (remaining 4397 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 12603 2.99 - 3.47: 24083 3.47 - 3.95: 40341 3.95 - 4.42: 44626 4.42 - 4.90: 75276 Nonbonded interactions: 196929 Sorted by model distance: nonbonded pdb=" OE2 GLU C 465 " pdb=" O3 NAG D 1 " model vdw 2.517 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.542 3.040 nonbonded pdb=" OE1 GLU B 298 " pdb=" OG SER B 316 " model vdw 2.542 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.542 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.544 3.040 ... (remaining 196924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 624 or resid 634 through 1311)) selection = (chain 'C' and (resid 27 through 624 or resid 634 through 1311)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.060 Find NCS groups from input model: 0.690 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 25308 Z= 0.770 Angle : 1.802 22.276 34554 Z= 1.178 Chirality : 0.103 1.524 4086 Planarity : 0.015 0.200 4353 Dihedral : 13.120 89.965 9974 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.76 % Favored : 92.81 % Rotamer: Outliers : 1.50 % Allowed : 3.27 % Favored : 95.23 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3003 helix: -0.80 (0.17), residues: 703 sheet: 0.20 (0.22), residues: 495 loop : -0.96 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 457 TYR 0.167 0.023 TYR A 904 PHE 0.111 0.011 PHE C 456 TRP 0.101 0.023 TRP A 886 HIS 0.012 0.003 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.01359 (25208) covalent geometry : angle 1.77427 (34293) SS BOND : bond 0.01256 ( 39) SS BOND : angle 2.16575 ( 78) hydrogen bonds : bond 0.16560 ( 1021) hydrogen bonds : angle 8.33662 ( 2841) link_BETA1-4 : bond 0.02582 ( 14) link_BETA1-4 : angle 5.07441 ( 42) link_NAG-ASN : bond 0.01001 ( 47) link_NAG-ASN : angle 4.45952 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 56 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8532 (p0) REVERT: A 486 PHE cc_start: 0.7810 (t80) cc_final: 0.7572 (t80) REVERT: B 421 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5626 (t80) REVERT: B 752 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8455 (tt) REVERT: C 96 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5352 (tp30) REVERT: C 869 MET cc_start: 0.9194 (mtt) cc_final: 0.8993 (mtm) outliers start: 40 outliers final: 11 residues processed: 96 average time/residue: 0.1849 time to fit residues: 27.5786 Evaluate side-chains 49 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A1010 GLN B 370 ASN B 394 ASN C 52 GLN C 675 GLN C 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.052575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038468 restraints weight = 160783.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039548 restraints weight = 81063.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040209 restraints weight = 53376.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.040628 restraints weight = 41597.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.040844 restraints weight = 35836.953| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25308 Z= 0.159 Angle : 0.736 12.735 34554 Z= 0.379 Chirality : 0.047 0.201 4086 Planarity : 0.004 0.077 4353 Dihedral : 7.276 58.329 4570 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 1.13 % Allowed : 4.88 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3003 helix: 1.42 (0.20), residues: 664 sheet: 0.09 (0.20), residues: 608 loop : -0.67 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.021 0.002 TYR A 265 PHE 0.021 0.002 PHE B 456 TRP 0.019 0.002 TRP C 64 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00351 (25208) covalent geometry : angle 0.69172 (34293) SS BOND : bond 0.00533 ( 39) SS BOND : angle 1.65310 ( 78) hydrogen bonds : bond 0.05175 ( 1021) hydrogen bonds : angle 6.16445 ( 2841) link_BETA1-4 : bond 0.00353 ( 14) link_BETA1-4 : angle 2.37117 ( 42) link_NAG-ASN : bond 0.00357 ( 47) link_NAG-ASN : angle 3.63070 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6238 (p) REVERT: A 486 PHE cc_start: 0.7930 (t80) cc_final: 0.7696 (t80) REVERT: B 365 TYR cc_start: 0.9056 (m-80) cc_final: 0.8827 (m-80) REVERT: B 421 TYR cc_start: 0.6537 (OUTLIER) cc_final: 0.5509 (t80) REVERT: B 752 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 96 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5940 (tp30) REVERT: C 369 TYR cc_start: 0.7641 (t80) cc_final: 0.7415 (t80) outliers start: 30 outliers final: 15 residues processed: 69 average time/residue: 0.1624 time to fit residues: 19.0092 Evaluate side-chains 54 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 107 optimal weight: 0.0980 chunk 291 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 394 ASN C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.052794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038819 restraints weight = 162093.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039910 restraints weight = 81440.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.040580 restraints weight = 53542.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041000 restraints weight = 41647.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.041217 restraints weight = 35800.197| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25308 Z= 0.121 Angle : 0.611 10.601 34554 Z= 0.317 Chirality : 0.045 0.225 4086 Planarity : 0.004 0.057 4353 Dihedral : 6.444 58.350 4564 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 1.28 % Allowed : 5.63 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3003 helix: 1.93 (0.21), residues: 672 sheet: 0.14 (0.20), residues: 601 loop : -0.55 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 237 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE C 135 TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00260 (25208) covalent geometry : angle 0.58011 (34293) SS BOND : bond 0.00416 ( 39) SS BOND : angle 1.61492 ( 78) hydrogen bonds : bond 0.04250 ( 1021) hydrogen bonds : angle 5.65157 ( 2841) link_BETA1-4 : bond 0.00469 ( 14) link_BETA1-4 : angle 1.87698 ( 42) link_NAG-ASN : bond 0.00216 ( 47) link_NAG-ASN : angle 2.69827 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 38 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 PHE cc_start: 0.7865 (t80) cc_final: 0.7619 (t80) REVERT: A 912 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 421 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.5391 (t80) REVERT: B 752 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 96 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6217 (tp30) outliers start: 34 outliers final: 16 residues processed: 70 average time/residue: 0.1552 time to fit residues: 18.1836 Evaluate side-chains 54 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 200 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 334 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.052027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.037928 restraints weight = 163848.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038999 restraints weight = 82418.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039671 restraints weight = 54416.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040068 restraints weight = 42340.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.040326 restraints weight = 36496.549| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25308 Z= 0.173 Angle : 0.605 10.007 34554 Z= 0.311 Chirality : 0.045 0.198 4086 Planarity : 0.004 0.054 4353 Dihedral : 6.196 58.014 4561 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 1.50 % Allowed : 6.42 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3003 helix: 1.88 (0.21), residues: 678 sheet: 0.13 (0.19), residues: 638 loop : -0.56 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE B 456 TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00398 (25208) covalent geometry : angle 0.57965 (34293) SS BOND : bond 0.00479 ( 39) SS BOND : angle 1.48956 ( 78) hydrogen bonds : bond 0.04259 ( 1021) hydrogen bonds : angle 5.57260 ( 2841) link_BETA1-4 : bond 0.00370 ( 14) link_BETA1-4 : angle 1.88338 ( 42) link_NAG-ASN : bond 0.00259 ( 47) link_NAG-ASN : angle 2.41529 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 34 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 PHE cc_start: 0.7860 (t80) cc_final: 0.7583 (t80) REVERT: B 421 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5080 (t80) REVERT: B 752 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8618 (tt) REVERT: C 369 TYR cc_start: 0.7393 (t80) cc_final: 0.6906 (m-80) REVERT: C 494 SER cc_start: 0.6357 (OUTLIER) cc_final: 0.6133 (t) outliers start: 40 outliers final: 23 residues processed: 70 average time/residue: 0.1654 time to fit residues: 19.4272 Evaluate side-chains 59 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 15 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.052059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.038080 restraints weight = 163388.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.039137 restraints weight = 82590.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039808 restraints weight = 54638.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.040214 restraints weight = 42501.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040427 restraints weight = 36595.738| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25308 Z= 0.140 Angle : 0.552 9.556 34554 Z= 0.285 Chirality : 0.044 0.195 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.886 58.720 4558 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.30 % Rotamer: Outliers : 1.46 % Allowed : 7.09 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3003 helix: 2.12 (0.21), residues: 669 sheet: 0.17 (0.19), residues: 639 loop : -0.55 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.001 PHE B 456 TRP 0.011 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (25208) covalent geometry : angle 0.53191 (34293) SS BOND : bond 0.00441 ( 39) SS BOND : angle 1.21300 ( 78) hydrogen bonds : bond 0.03890 ( 1021) hydrogen bonds : angle 5.35848 ( 2841) link_BETA1-4 : bond 0.00340 ( 14) link_BETA1-4 : angle 1.62234 ( 42) link_NAG-ASN : bond 0.00165 ( 47) link_NAG-ASN : angle 2.04473 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 36 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.4944 (t80) REVERT: B 454 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7249 (ttt180) REVERT: B 752 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (tt) REVERT: C 369 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: C 462 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8538 (tmtt) REVERT: C 494 SER cc_start: 0.6433 (OUTLIER) cc_final: 0.6216 (t) outliers start: 39 outliers final: 23 residues processed: 72 average time/residue: 0.1719 time to fit residues: 20.0687 Evaluate side-chains 59 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 193 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.052299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038361 restraints weight = 163751.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039434 restraints weight = 82392.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040117 restraints weight = 54308.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.040487 restraints weight = 42076.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.040762 restraints weight = 36461.079| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25308 Z= 0.112 Angle : 0.535 10.208 34554 Z= 0.276 Chirality : 0.043 0.198 4086 Planarity : 0.003 0.051 4353 Dihedral : 5.560 58.659 4556 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 1.28 % Allowed : 7.70 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3003 helix: 2.20 (0.21), residues: 676 sheet: 0.24 (0.19), residues: 643 loop : -0.50 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE B 456 TRP 0.010 0.001 TRP B 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00251 (25208) covalent geometry : angle 0.51522 (34293) SS BOND : bond 0.00347 ( 39) SS BOND : angle 1.59611 ( 78) hydrogen bonds : bond 0.03701 ( 1021) hydrogen bonds : angle 5.24689 ( 2841) link_BETA1-4 : bond 0.00358 ( 14) link_BETA1-4 : angle 1.52542 ( 42) link_NAG-ASN : bond 0.00160 ( 47) link_NAG-ASN : angle 1.89117 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 33 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.5143 (t80) REVERT: B 454 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7275 (ttt180) REVERT: B 752 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 369 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6948 (m-80) outliers start: 34 outliers final: 24 residues processed: 65 average time/residue: 0.1576 time to fit residues: 17.3097 Evaluate side-chains 59 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 24 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 241 optimal weight: 50.0000 chunk 261 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 157 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.051448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037389 restraints weight = 164560.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038428 restraints weight = 83920.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.039075 restraints weight = 55824.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039475 restraints weight = 43703.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.039717 restraints weight = 37729.982| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25308 Z= 0.223 Angle : 0.606 11.357 34554 Z= 0.310 Chirality : 0.045 0.217 4086 Planarity : 0.004 0.053 4353 Dihedral : 5.759 58.261 4556 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 1.43 % Allowed : 7.85 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3003 helix: 2.00 (0.21), residues: 676 sheet: 0.12 (0.19), residues: 642 loop : -0.59 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.002 PHE B 456 TRP 0.009 0.001 TRP C 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00520 (25208) covalent geometry : angle 0.58572 (34293) SS BOND : bond 0.00390 ( 39) SS BOND : angle 1.67544 ( 78) hydrogen bonds : bond 0.04257 ( 1021) hydrogen bonds : angle 5.46950 ( 2841) link_BETA1-4 : bond 0.00324 ( 14) link_BETA1-4 : angle 1.76206 ( 42) link_NAG-ASN : bond 0.00295 ( 47) link_NAG-ASN : angle 2.03567 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 31 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8816 (pp) REVERT: B 421 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.4775 (t80) REVERT: B 454 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7032 (ttt90) REVERT: B 752 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8591 (tt) REVERT: C 369 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7038 (m-80) outliers start: 38 outliers final: 28 residues processed: 65 average time/residue: 0.1506 time to fit residues: 16.9539 Evaluate side-chains 64 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 212 optimal weight: 0.1980 chunk 271 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 293 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 102 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.051761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037793 restraints weight = 163391.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038843 restraints weight = 82909.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039509 restraints weight = 54934.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039910 restraints weight = 42787.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040135 restraints weight = 36881.971| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25308 Z= 0.151 Angle : 0.547 9.593 34554 Z= 0.281 Chirality : 0.043 0.224 4086 Planarity : 0.003 0.054 4353 Dihedral : 5.585 57.944 4556 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 1.31 % Allowed : 8.22 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3003 helix: 2.17 (0.21), residues: 670 sheet: 0.15 (0.19), residues: 645 loop : -0.58 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 456 TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00345 (25208) covalent geometry : angle 0.52808 (34293) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.50899 ( 78) hydrogen bonds : bond 0.03903 ( 1021) hydrogen bonds : angle 5.33315 ( 2841) link_BETA1-4 : bond 0.00359 ( 14) link_BETA1-4 : angle 1.56875 ( 42) link_NAG-ASN : bond 0.00169 ( 47) link_NAG-ASN : angle 1.85781 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 31 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 421 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.4888 (t80) REVERT: B 752 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 369 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7008 (m-80) outliers start: 35 outliers final: 29 residues processed: 63 average time/residue: 0.1431 time to fit residues: 16.0445 Evaluate side-chains 64 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 26 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 655 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.051710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037712 restraints weight = 164242.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038790 restraints weight = 81995.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039463 restraints weight = 53849.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.039866 restraints weight = 41701.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040121 restraints weight = 35835.270| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25308 Z= 0.150 Angle : 0.542 8.486 34554 Z= 0.279 Chirality : 0.043 0.220 4086 Planarity : 0.003 0.053 4353 Dihedral : 5.466 57.849 4556 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 1.35 % Allowed : 8.30 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3003 helix: 2.21 (0.21), residues: 671 sheet: 0.21 (0.19), residues: 646 loop : -0.59 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 456 TRP 0.008 0.001 TRP C 64 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00345 (25208) covalent geometry : angle 0.52431 (34293) SS BOND : bond 0.00367 ( 39) SS BOND : angle 1.50163 ( 78) hydrogen bonds : bond 0.03876 ( 1021) hydrogen bonds : angle 5.28712 ( 2841) link_BETA1-4 : bond 0.00366 ( 14) link_BETA1-4 : angle 1.58156 ( 42) link_NAG-ASN : bond 0.00178 ( 47) link_NAG-ASN : angle 1.77658 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 32 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8698 (pp) REVERT: B 421 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.4763 (t80) REVERT: B 752 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8544 (tt) REVERT: C 369 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.7050 (m-80) outliers start: 36 outliers final: 29 residues processed: 65 average time/residue: 0.1551 time to fit residues: 17.6929 Evaluate side-chains 64 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.0870 chunk 289 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.051919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037982 restraints weight = 163882.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.039065 restraints weight = 81609.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.039731 restraints weight = 53223.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.040147 restraints weight = 41364.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.040362 restraints weight = 35570.755| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25308 Z= 0.121 Angle : 0.520 8.542 34554 Z= 0.268 Chirality : 0.043 0.220 4086 Planarity : 0.003 0.052 4353 Dihedral : 5.331 57.294 4556 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 1.31 % Allowed : 8.41 % Favored : 90.28 % 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: 0.42 (0.15), residues: 3003 helix: 2.30 (0.21), residues: 672 sheet: 0.28 (0.20), residues: 634 loop : -0.54 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.018 0.001 TYR C1067 PHE 0.017 0.001 PHE B 456 TRP 0.007 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00275 (25208) covalent geometry : angle 0.50376 (34293) SS BOND : bond 0.00310 ( 39) SS BOND : angle 1.38961 ( 78) hydrogen bonds : bond 0.03691 ( 1021) hydrogen bonds : angle 5.19444 ( 2841) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 1.48267 ( 42) link_NAG-ASN : bond 0.00150 ( 47) link_NAG-ASN : angle 1.69131 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 32 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8696 (pp) REVERT: A 461 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7419 (mm) REVERT: B 421 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.4723 (t80) REVERT: B 752 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8573 (tt) REVERT: C 369 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7087 (m-80) outliers start: 35 outliers final: 27 residues processed: 64 average time/residue: 0.1533 time to fit residues: 17.0330 Evaluate side-chains 63 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 229 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C 422 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.052460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038676 restraints weight = 163912.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039769 restraints weight = 81114.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.040431 restraints weight = 52923.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.040860 restraints weight = 41025.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.041076 restraints weight = 35133.787| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25308 Z= 0.090 Angle : 0.492 8.576 34554 Z= 0.254 Chirality : 0.043 0.259 4086 Planarity : 0.003 0.052 4353 Dihedral : 4.932 56.311 4552 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 1.09 % Allowed : 8.63 % Favored : 90.28 % 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: 0.55 (0.16), residues: 3003 helix: 2.45 (0.21), residues: 671 sheet: 0.37 (0.20), residues: 640 loop : -0.48 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE B 456 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00195 (25208) covalent geometry : angle 0.47818 (34293) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.21386 ( 78) hydrogen bonds : bond 0.03349 ( 1021) hydrogen bonds : angle 4.97319 ( 2841) link_BETA1-4 : bond 0.00380 ( 14) link_BETA1-4 : angle 1.33472 ( 42) link_NAG-ASN : bond 0.00183 ( 47) link_NAG-ASN : angle 1.51341 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4004.58 seconds wall clock time: 70 minutes 1.34 seconds (4201.34 seconds total)