Starting phenix.real_space_refine on Sun Jul 5 02:05:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toy_26041/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.cif" model { file = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_2026/7toy_26041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toy_26041/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 11 Time building chain proxies: 4.92, per 1000 atoms: 0.20 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: 1.67 Conformation dependent library (CDL) restraints added in 948.6 milliseconds 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: 0.70 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: 4.97 Time building geometry restraints manager: 2.22 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: 13466 17.99 - 35.99: 823 35.99 - 53.98: 147 53.98 - 71.97: 52 71.97 - 89.97: 36 Dihedral angle restraints: 14524 sinusoidal: 5652 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 14521 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.160 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 13.682 89.965 8693 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/Z covalent geometry : bond 0.01359 / 0.77 (25208) covalent geometry : angle 1.77427 / 1.18 (34293) SS BOND : bond 0.01256 / 0.70 ( 39) SS BOND : angle 2.16575 / 1.44 ( 78) hydrogen bonds : bond 0.16560 / 10.80 ( 1021) hydrogen bonds : angle 8.33662 / 5.76 ( 2841) link_BETA1-4 : bond 0.02582 / 1.54 ( 14) link_BETA1-4 : angle 5.07441 / 3.14 ( 42) link_NAG-ASN : bond 0.01001 / 0.72 ( 47) link_NAG-ASN : angle 4.45952 / 3.06 ( 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 : 0.824 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: 0.1699 time to fit residues: 25.3145 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 : 0.832 ------------------------------------------------------------------------------- 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... A 607 GLN A 955 ASN A1010 GLN B 370 ASN B 394 ASN C 52 GLN C 675 GLN C 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.052603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038521 restraints weight = 160760.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039599 restraints weight = 80473.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040269 restraints weight = 53027.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.040673 restraints weight = 41286.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.040920 restraints weight = 35543.981| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25308 Z= 0.160 Angle : 0.729 10.954 34554 Z= 0.374 Chirality : 0.047 0.190 4086 Planarity : 0.004 0.072 4353 Dihedral : 7.035 57.926 3289 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 1.24 % Allowed : 4.77 % 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: -0.05 (0.15), residues: 3003 helix: 1.41 (0.20), residues: 665 sheet: 0.13 (0.20), residues: 611 loop : -0.66 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.021 0.002 TYR A 265 PHE 0.022 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/Z covalent geometry : bond 0.00354 / 0.16 (25208) covalent geometry : angle 0.69083 / 0.37 (34293) SS BOND : bond 0.00478 / 0.28 ( 39) SS BOND : angle 1.62364 / 1.03 ( 78) hydrogen bonds : bond 0.05042 / 3.30 ( 1021) hydrogen bonds : angle 6.11791 / 4.23 ( 2841) link_BETA1-4 : bond 0.00475 / 0.30 ( 14) link_BETA1-4 : angle 2.05582 / 1.33 ( 42) link_NAG-ASN : bond 0.00343 / 0.19 ( 47) link_NAG-ASN : angle 3.36436 / 2.32 ( 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 74 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6222 (p) REVERT: A 486 PHE cc_start: 0.7890 (t80) cc_final: 0.7654 (t80) REVERT: B 365 TYR cc_start: 0.9043 (m-80) cc_final: 0.8842 (m-80) REVERT: B 421 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5334 (t80) REVERT: B 752 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8612 (tt) REVERT: C 96 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5930 (tp30) REVERT: C 369 TYR cc_start: 0.7594 (t80) cc_final: 0.7380 (t80) outliers start: 33 outliers final: 16 residues processed: 73 average time/residue: 0.1520 time to fit residues: 18.6794 Evaluate side-chains 55 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 291 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037742 restraints weight = 161950.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038804 restraints weight = 81325.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039467 restraints weight = 53674.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039857 restraints weight = 41895.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040114 restraints weight = 36258.764| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25308 Z= 0.173 Angle : 0.649 10.558 34554 Z= 0.334 Chirality : 0.046 0.207 4086 Planarity : 0.004 0.064 4353 Dihedral : 6.252 58.087 3283 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 1.43 % Allowed : 5.63 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3003 helix: 1.83 (0.21), residues: 669 sheet: 0.02 (0.20), residues: 607 loop : -0.62 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 237 TYR 0.019 0.002 TYR C1067 PHE 0.030 0.002 PHE C 135 TRP 0.014 0.002 TRP C 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (25208) covalent geometry : angle 0.62092 / 0.33 (34293) SS BOND : bond 0.00439 / 0.29 ( 39) SS BOND : angle 1.70085 / 1.03 ( 78) hydrogen bonds : bond 0.04601 / 3.01 ( 1021) hydrogen bonds : angle 5.79185 / 3.99 ( 2841) link_BETA1-4 : bond 0.00384 / 0.21 ( 14) link_BETA1-4 : angle 1.76390 / 1.14 ( 42) link_NAG-ASN : bond 0.00256 / 0.15 ( 47) link_NAG-ASN : angle 2.60556 / 1.80 ( 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: 38 poor density : 34 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8956 (m-80) cc_final: 0.8754 (m-80) REVERT: B 421 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5288 (t80) REVERT: B 752 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 96 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6164 (tp30) REVERT: C 494 SER cc_start: 0.6626 (OUTLIER) cc_final: 0.6393 (t) outliers start: 38 outliers final: 16 residues processed: 70 average time/residue: 0.1417 time to fit residues: 17.2959 Evaluate side-chains 53 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 635 VAL Chi-restraints excluded: chain A residue 886 TRP 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 96 GLU 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 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 200 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 235 optimal weight: 40.0000 chunk 220 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 251 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN B 334 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.052193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038192 restraints weight = 162731.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039266 restraints weight = 82310.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039914 restraints weight = 54285.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.040340 restraints weight = 42425.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.040576 restraints weight = 36450.847| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25308 Z= 0.139 Angle : 0.575 9.904 34554 Z= 0.296 Chirality : 0.044 0.202 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.800 58.128 3282 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 1.54 % Allowed : 6.49 % Favored : 91.97 % 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: 0.26 (0.15), residues: 3003 helix: 2.00 (0.21), residues: 670 sheet: 0.14 (0.19), residues: 642 loop : -0.55 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (25208) covalent geometry : angle 0.55454 / 0.29 (34293) SS BOND : bond 0.00509 / 0.34 ( 39) SS BOND : angle 1.36358 / 0.84 ( 78) hydrogen bonds : bond 0.04008 / 2.62 ( 1021) hydrogen bonds : angle 5.48694 / 3.78 ( 2841) link_BETA1-4 : bond 0.00335 / 0.19 ( 14) link_BETA1-4 : angle 1.49856 / 0.97 ( 42) link_NAG-ASN : bond 0.00171 / 0.10 ( 47) link_NAG-ASN : angle 2.14918 / 1.46 ( 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 77 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 36 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 PHE cc_start: 0.7753 (t80) cc_final: 0.7550 (t80) REVERT: B 421 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5017 (t80) REVERT: B 454 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7296 (ttt180) REVERT: B 752 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8613 (tt) REVERT: C 369 TYR cc_start: 0.7434 (t80) cc_final: 0.6941 (m-80) outliers start: 41 outliers final: 25 residues processed: 76 average time/residue: 0.1548 time to fit residues: 19.9695 Evaluate side-chains 61 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 33 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1104 VAL 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 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 320 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 15 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 236 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.051271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037111 restraints weight = 162821.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038149 restraints weight = 82921.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038803 restraints weight = 54981.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039189 restraints weight = 42916.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039437 restraints weight = 37064.077| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25308 Z= 0.246 Angle : 0.650 9.467 34554 Z= 0.333 Chirality : 0.046 0.203 4086 Planarity : 0.004 0.064 4353 Dihedral : 5.813 59.343 3277 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.00 % Rotamer: Outliers : 1.54 % Allowed : 7.09 % Favored : 91.37 % 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: 0.04 (0.15), residues: 3003 helix: 1.80 (0.21), residues: 675 sheet: -0.01 (0.19), residues: 634 loop : -0.69 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.020 0.002 TYR C1067 PHE 0.020 0.002 PHE B 456 TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (25208) covalent geometry : angle 0.63027 / 0.33 (34293) SS BOND : bond 0.00461 / 0.30 ( 39) SS BOND : angle 1.37352 / 0.86 ( 78) hydrogen bonds : bond 0.04573 / 3.00 ( 1021) hydrogen bonds : angle 5.73203 / 3.95 ( 2841) link_BETA1-4 : bond 0.00359 / 0.19 ( 14) link_BETA1-4 : angle 1.71455 / 1.13 ( 42) link_NAG-ASN : bond 0.00365 / 0.22 ( 47) link_NAG-ASN : angle 2.24668 / 1.54 ( 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: 41 poor density : 34 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8636 (m-80) cc_final: 0.8435 (m-80) REVERT: A 486 PHE cc_start: 0.7858 (t80) cc_final: 0.7657 (t80) REVERT: B 421 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5092 (t80) REVERT: B 752 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 369 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: C 462 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8466 (tmtt) outliers start: 41 outliers final: 27 residues processed: 71 average time/residue: 0.1539 time to fit residues: 19.2254 Evaluate side-chains 62 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 32 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR 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 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 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 16 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN B 207 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 = 0.3531 r_free = 0.3531 target = 0.051789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037810 restraints weight = 164038.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038857 restraints weight = 82790.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039511 restraints weight = 54754.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039932 restraints weight = 42729.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040161 restraints weight = 36711.135| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2820 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= 0.136 Angle : 0.553 9.269 34554 Z= 0.285 Chirality : 0.044 0.204 4086 Planarity : 0.004 0.055 4353 Dihedral : 5.495 58.305 3277 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 1.28 % Allowed : 7.85 % Favored : 90.88 % 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: 2.09 (0.21), residues: 669 sheet: 0.10 (0.19), residues: 643 loop : -0.62 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.001 PHE B 456 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (25208) covalent geometry : angle 0.53537 / 0.28 (34293) SS BOND : bond 0.00379 / 0.24 ( 39) SS BOND : angle 1.41200 / 0.86 ( 78) hydrogen bonds : bond 0.03894 / 2.54 ( 1021) hydrogen bonds : angle 5.41274 / 3.73 ( 2841) link_BETA1-4 : bond 0.00357 / 0.20 ( 14) link_BETA1-4 : angle 1.38404 / 0.90 ( 42) link_NAG-ASN : bond 0.00171 / 0.10 ( 47) link_NAG-ASN : angle 1.89583 / 1.29 ( 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 68 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 34 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 486 PHE cc_start: 0.7870 (t80) cc_final: 0.7652 (t80) REVERT: B 421 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.4788 (t80) REVERT: B 454 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7036 (ttt90) REVERT: B 752 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8574 (tt) REVERT: C 369 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.7064 (m-80) outliers start: 34 outliers final: 22 residues processed: 67 average time/residue: 0.1591 time to fit residues: 18.6904 Evaluate side-chains 57 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 30 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR 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 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 351 TYR Chi-restraints excluded: chain C residue 369 TYR 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: 0.5980 chunk 284 optimal weight: 4.9990 chunk 241 optimal weight: 0.0270 chunk 261 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.051669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.037688 restraints weight = 163911.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038736 restraints weight = 83048.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039376 restraints weight = 54897.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039786 restraints weight = 42913.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040034 restraints weight = 37040.480| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25308 Z= 0.148 Angle : 0.550 8.820 34554 Z= 0.282 Chirality : 0.044 0.216 4086 Planarity : 0.004 0.054 4353 Dihedral : 5.336 58.191 3275 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 1.43 % Allowed : 8.18 % Favored : 90.39 % 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: 0.25 (0.15), residues: 3003 helix: 2.15 (0.21), residues: 669 sheet: 0.11 (0.19), residues: 653 loop : -0.63 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 456 TRP 0.010 0.001 TRP C 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (25208) covalent geometry : angle 0.53325 / 0.28 (34293) SS BOND : bond 0.00390 / 0.26 ( 39) SS BOND : angle 1.27881 / 0.78 ( 78) hydrogen bonds : bond 0.03901 / 2.55 ( 1021) hydrogen bonds : angle 5.34958 / 3.69 ( 2841) link_BETA1-4 : bond 0.00298 / 0.16 ( 14) link_BETA1-4 : angle 1.41196 / 0.92 ( 42) link_NAG-ASN : bond 0.00190 / 0.12 ( 47) link_NAG-ASN : angle 1.82958 / 1.25 ( 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 : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8805 (pp) REVERT: A 486 PHE cc_start: 0.7915 (t80) cc_final: 0.7699 (t80) REVERT: B 421 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.4791 (t80) REVERT: B 454 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7039 (ttt90) REVERT: B 752 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8573 (tt) REVERT: C 369 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7090 (m-80) outliers start: 38 outliers final: 29 residues processed: 67 average time/residue: 0.1519 time to fit residues: 18.0167 Evaluate side-chains 65 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 31 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 912 THR 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 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 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 738 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 212 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 293 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS C 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.051336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037291 restraints weight = 164078.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038338 restraints weight = 82816.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038979 restraints weight = 54786.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039400 restraints weight = 42768.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.039631 restraints weight = 36737.270| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25308 Z= 0.191 Angle : 0.576 8.663 34554 Z= 0.295 Chirality : 0.044 0.215 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.386 58.496 3275 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 1.50 % Allowed : 8.33 % Favored : 90.17 % 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: 0.18 (0.15), residues: 3003 helix: 2.06 (0.21), residues: 669 sheet: 0.07 (0.19), residues: 645 loop : -0.66 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.019 0.001 PHE B 456 TRP 0.008 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (25208) covalent geometry : angle 0.56014 / 0.29 (34293) SS BOND : bond 0.00417 / 0.27 ( 39) SS BOND : angle 1.26964 / 0.78 ( 78) hydrogen bonds : bond 0.04137 / 2.71 ( 1021) hydrogen bonds : angle 5.46254 / 3.76 ( 2841) link_BETA1-4 : bond 0.00331 / 0.17 ( 14) link_BETA1-4 : angle 1.47455 / 0.96 ( 42) link_NAG-ASN : bond 0.00239 / 0.14 ( 47) link_NAG-ASN : angle 1.85007 / 1.26 ( 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 71 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 31 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 461 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7593 (mm) REVERT: A 486 PHE cc_start: 0.7929 (t80) cc_final: 0.7703 (t80) REVERT: B 323 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9201 (p) REVERT: B 421 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.5212 (t80) REVERT: B 752 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 786 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7825 (pmtt) REVERT: C 369 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7143 (m-80) outliers start: 40 outliers final: 28 residues processed: 69 average time/residue: 0.1505 time to fit residues: 18.6201 Evaluate side-chains 65 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 30 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 312 ILE 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 620 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR 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 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 786 LYS 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 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 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: 6.9990 chunk 56 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037132 restraints weight = 164850.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038163 restraints weight = 83914.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038812 restraints weight = 55636.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039214 restraints weight = 43366.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039437 restraints weight = 37423.654| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25308 Z= 0.212 Angle : 0.602 8.918 34554 Z= 0.308 Chirality : 0.045 0.348 4086 Planarity : 0.004 0.057 4353 Dihedral : 5.428 58.275 3275 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 1.46 % Allowed : 8.75 % Favored : 89.79 % 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: 0.11 (0.15), residues: 3003 helix: 2.03 (0.21), residues: 669 sheet: 0.03 (0.19), residues: 657 loop : -0.72 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.019 0.001 PHE B 456 TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (25208) covalent geometry : angle 0.58562 / 0.30 (34293) SS BOND : bond 0.00516 / 0.37 ( 39) SS BOND : angle 1.44578 / 0.92 ( 78) hydrogen bonds : bond 0.04238 / 2.78 ( 1021) hydrogen bonds : angle 5.50698 / 3.79 ( 2841) link_BETA1-4 : bond 0.00304 / 0.16 ( 14) link_BETA1-4 : angle 1.50200 / 0.98 ( 42) link_NAG-ASN : bond 0.00318 / 0.21 ( 47) link_NAG-ASN : angle 1.87450 / 1.28 ( 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 69 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 30 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8820 (pp) REVERT: A 461 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 323 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9199 (p) REVERT: B 421 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.5027 (t80) REVERT: B 752 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8574 (tt) REVERT: B 786 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7823 (pmtt) REVERT: C 369 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.7185 (m-80) outliers start: 39 outliers final: 28 residues processed: 68 average time/residue: 0.1481 time to fit residues: 18.2682 Evaluate side-chains 65 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 30 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 312 ILE 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 912 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR 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 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 786 LYS 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 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL 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: 0.0370 chunk 289 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.052095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038275 restraints weight = 163700.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039357 restraints weight = 80828.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.040045 restraints weight = 52508.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.040445 restraints weight = 40579.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.040659 restraints weight = 34905.820| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25308 Z= 0.099 Angle : 0.515 8.913 34554 Z= 0.265 Chirality : 0.043 0.246 4086 Planarity : 0.004 0.055 4353 Dihedral : 5.100 57.837 3275 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 1.05 % Allowed : 9.01 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3003 helix: 2.34 (0.21), residues: 664 sheet: 0.23 (0.19), residues: 641 loop : -0.62 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE B 456 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (25208) covalent geometry : angle 0.50287 / 0.26 (34293) SS BOND : bond 0.00433 / 0.31 ( 39) SS BOND : angle 1.22735 / 0.77 ( 78) hydrogen bonds : bond 0.03485 / 2.28 ( 1021) hydrogen bonds : angle 5.13443 / 3.54 ( 2841) link_BETA1-4 : bond 0.00343 / 0.20 ( 14) link_BETA1-4 : angle 1.17208 / 0.75 ( 42) link_NAG-ASN : bond 0.00222 / 0.13 ( 47) link_NAG-ASN : angle 1.52198 / 1.02 ( 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 60 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8717 (pp) REVERT: A 461 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7640 (mm) REVERT: B 323 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9227 (p) REVERT: B 421 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.4992 (t80) REVERT: B 752 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 369 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (m-80) outliers start: 28 outliers final: 21 residues processed: 59 average time/residue: 0.1397 time to fit residues: 14.8533 Evaluate side-chains 57 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 30 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL 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 912 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR 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 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 752 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 615 VAL 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: 6.9990 chunk 193 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 267 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.051428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037496 restraints weight = 164390.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038529 restraints weight = 83109.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039167 restraints weight = 55090.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.039579 restraints weight = 43058.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039813 restraints weight = 37087.502| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25308 Z= 0.174 Angle : 0.556 8.636 34554 Z= 0.285 Chirality : 0.044 0.240 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.164 57.613 3273 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.01 % Allowed : 9.23 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3003 helix: 2.28 (0.21), residues: 670 sheet: 0.19 (0.19), residues: 637 loop : -0.62 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.019 0.001 TYR C1067 PHE 0.017 0.001 PHE B 456 TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (25208) covalent geometry : angle 0.54229 / 0.28 (34293) SS BOND : bond 0.00401 / 0.26 ( 39) SS BOND : angle 1.30565 / 0.82 ( 78) hydrogen bonds : bond 0.03906 / 2.56 ( 1021) hydrogen bonds : angle 5.28119 / 3.65 ( 2841) link_BETA1-4 : bond 0.00302 / 0.15 ( 14) link_BETA1-4 : angle 1.36906 / 0.89 ( 42) link_NAG-ASN : bond 0.00226 / 0.14 ( 47) link_NAG-ASN : angle 1.65630 / 1.13 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.08 seconds wall clock time: 69 minutes 38.68 seconds (4178.68 seconds total)