Starting phenix.real_space_refine on Sat Jun 21 13:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_26041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_26041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_26041.map" model { file = "/net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_26041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toy_26041/06_2025/7toy_26041.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24673 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7910 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 7 Chain: "B" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7924 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.10, per 1000 atoms: 0.57 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: 5.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5714 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 46 sheets defined 27.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 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: 10.21 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7431 1.34 - 1.46: 4716 1.46 - 1.59: 12932 1.59 - 1.71: 0 1.71 - 1.84: 129 Bond restraints: 25208 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.495 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.494 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.493 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 25203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 33803 4.46 - 8.91: 482 8.91 - 13.37: 7 13.37 - 17.82: 0 17.82 - 22.28: 1 Bond angle restraints: 34293 Sorted by residual: angle pdb=" CA VAL A 635 " pdb=" CB VAL A 635 " pdb=" CG1 VAL A 635 " ideal model delta sigma weight residual 110.40 132.68 -22.28 1.70e+00 3.46e-01 1.72e+02 angle pdb=" N ARG B 454 " pdb=" CA ARG B 454 " pdb=" C ARG B 454 " ideal model delta sigma weight residual 111.40 120.06 -8.66 1.22e+00 6.72e-01 5.03e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.54 -10.47 1.52e+00 4.33e-01 4.75e+01 angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 108.79 118.80 -10.01 1.53e+00 4.27e-01 4.28e+01 angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.25 6.35 1.00e+00 1.00e+00 4.03e+01 ... (remaining 34288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14686 17.99 - 35.99: 874 35.99 - 53.98: 157 53.98 - 71.97: 52 71.97 - 89.97: 36 Dihedral angle restraints: 15805 sinusoidal: 6933 harmonic: 8872 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.93 82.93 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.09 57.09 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" C ARG C 457 " pdb=" N ARG C 457 " pdb=" CA ARG C 457 " pdb=" CB ARG C 457 " ideal model delta harmonic sigma weight residual -122.60 -138.26 15.66 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 15802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4070 0.305 - 0.610: 15 0.610 - 0.914: 0 0.914 - 1.219: 0 1.219 - 1.524: 1 Chirality restraints: 4086 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.53e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.45e+01 ... (remaining 4083 not shown) Planarity restraints: 4400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.141 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" CG ASN B 657 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.137 2.00e-02 2.50e+03 1.45e-01 2.64e+02 pdb=" CG ASN C 616 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.135 2.00e-02 2.50e+03 1.42e-01 2.51e+02 pdb=" CG ASN A 165 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.214 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.169 2.00e-02 2.50e+03 ... (remaining 4397 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 12603 2.99 - 3.47: 24083 3.47 - 3.95: 40341 3.95 - 4.42: 44626 4.42 - 4.90: 75276 Nonbonded interactions: 196929 Sorted by model distance: nonbonded pdb=" OE2 GLU C 465 " pdb=" O3 NAG D 1 " model vdw 2.517 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.542 3.040 nonbonded pdb=" OE1 GLU B 298 " pdb=" OG SER B 316 " model vdw 2.542 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.542 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.544 3.040 ... (remaining 196924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 624 or resid 634 through 1147 or resid 1301 thr \ ough 1311)) selection = (chain 'C' and (resid 27 through 624 or resid 634 through 1147 or resid 1301 thr \ ough 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 54.330 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.086 25308 Z= 0.770 Angle : 1.802 22.276 34554 Z= 1.178 Chirality : 0.103 1.524 4086 Planarity : 0.015 0.200 4353 Dihedral : 13.120 89.965 9974 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.101 0.023 TRP A 886 HIS 0.012 0.003 HIS B 519 PHE 0.111 0.011 PHE C 456 TYR 0.167 0.023 TYR A 904 ARG 0.016 0.002 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01001 ( 47) link_NAG-ASN : angle 4.45952 ( 141) link_BETA1-4 : bond 0.02582 ( 14) link_BETA1-4 : angle 5.07441 ( 42) hydrogen bonds : bond 0.16560 ( 1021) hydrogen bonds : angle 8.33662 ( 2841) SS BOND : bond 0.01256 ( 39) SS BOND : angle 2.16575 ( 78) covalent geometry : bond 0.01359 (25208) covalent geometry : angle 1.77427 (34293) *********************** 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 : 2.488 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: 0.5375 (tp30) REVERT: C 869 MET cc_start: 0.9194 (mtt) cc_final: 0.8992 (mtm) outliers start: 40 outliers final: 11 residues processed: 96 average time/residue: 0.4683 time to fit residues: 71.2501 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 : 2.582 ------------------------------------------------------------------------------- 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 256 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3562 r_free = 0.3562 target = 0.053040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038980 restraints weight = 161536.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040071 restraints weight = 80878.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.040745 restraints weight = 53142.492| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25308 Z= 0.140 Angle : 0.712 12.179 34554 Z= 0.366 Chirality : 0.046 0.207 4086 Planarity : 0.004 0.072 4353 Dihedral : 7.181 58.669 4570 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.30 % Favored : 96.50 % Rotamer: Outliers : 1.20 % Allowed : 4.69 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3003 helix: 1.52 (0.20), residues: 665 sheet: 0.16 (0.20), residues: 598 loop : -0.63 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 64 HIS 0.003 0.001 HIS B1048 PHE 0.022 0.002 PHE B 456 TYR 0.022 0.002 TYR A 265 ARG 0.007 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 47) link_NAG-ASN : angle 3.51139 ( 141) link_BETA1-4 : bond 0.00433 ( 14) link_BETA1-4 : angle 2.23031 ( 42) hydrogen bonds : bond 0.04910 ( 1021) hydrogen bonds : angle 6.06630 ( 2841) SS BOND : bond 0.00484 ( 39) SS BOND : angle 1.52816 ( 78) covalent geometry : bond 0.00292 (25208) covalent geometry : angle 0.66939 (34293) *********************** 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 75 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 43 time to evaluate : 2.898 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: 0.7126 (OUTLIER) cc_final: 0.6186 (p) REVERT: A 486 PHE cc_start: 0.8018 (t80) cc_final: 0.7792 (t80) REVERT: A 1050 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7834 (ttp) REVERT: B 365 TYR cc_start: 0.9094 (m-80) cc_final: 0.8834 (m-80) REVERT: B 421 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5380 (t80) REVERT: B 752 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8608 (tt) REVERT: C 96 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5931 (tp30) REVERT: C 369 TYR cc_start: 0.7701 (t80) cc_final: 0.7483 (t80) REVERT: C 1050 MET cc_start: 0.8132 (ttm) cc_final: 0.7931 (ttm) outliers start: 32 outliers final: 16 residues processed: 74 average time/residue: 0.3756 time to fit residues: 47.4534 Evaluate side-chains 58 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 A residue 1050 MET 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 141 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN C 66 HIS C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.051494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037315 restraints weight = 162154.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.038356 restraints weight = 82495.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039020 restraints weight = 54844.913| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 25308 Z= 0.257 Angle : 0.720 10.523 34554 Z= 0.369 Chirality : 0.048 0.216 4086 Planarity : 0.004 0.062 4353 Dihedral : 6.828 57.964 4564 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.00 % Rotamer: Outliers : 1.43 % Allowed : 5.89 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3003 helix: 1.65 (0.21), residues: 664 sheet: -0.09 (0.20), residues: 606 loop : -0.71 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 64 HIS 0.007 0.001 HIS B1064 PHE 0.026 0.002 PHE C 135 TYR 0.020 0.002 TYR A1067 ARG 0.011 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 47) link_NAG-ASN : angle 2.93083 ( 141) link_BETA1-4 : bond 0.00543 ( 14) link_BETA1-4 : angle 2.17923 ( 42) hydrogen bonds : bond 0.05033 ( 1021) hydrogen bonds : angle 5.98307 ( 2841) SS BOND : bond 0.00645 ( 39) SS BOND : angle 1.73902 ( 78) covalent geometry : bond 0.00600 (25208) covalent geometry : angle 0.68884 (34293) *********************** 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 : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.9059 (m-80) cc_final: 0.8843 (m-80) REVERT: B 421 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.5421 (t80) REVERT: B 752 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8619 (tt) REVERT: C 96 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6463 (tp30) REVERT: C 494 SER cc_start: 0.6652 (OUTLIER) cc_final: 0.6399 (t) outliers start: 38 outliers final: 16 residues processed: 71 average time/residue: 0.3223 time to fit residues: 40.7938 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 : 2.979 ------------------------------------------------------------------------------- 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 278 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 43 optimal weight: 0.0060 chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 226 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.052630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038703 restraints weight = 163915.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039808 restraints weight = 81176.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.040502 restraints weight = 52852.827| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25308 Z= 0.104 Angle : 0.566 10.069 34554 Z= 0.292 Chirality : 0.044 0.214 4086 Planarity : 0.004 0.054 4353 Dihedral : 6.155 58.043 4563 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 1.31 % Allowed : 6.53 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3003 helix: 2.06 (0.21), residues: 670 sheet: 0.11 (0.19), residues: 634 loop : -0.54 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.002 0.000 HIS C1048 PHE 0.020 0.001 PHE B 456 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 47) link_NAG-ASN : angle 2.27258 ( 141) link_BETA1-4 : bond 0.00439 ( 14) link_BETA1-4 : angle 1.59996 ( 42) hydrogen bonds : bond 0.03827 ( 1021) hydrogen bonds : angle 5.42121 ( 2841) SS BOND : bond 0.00373 ( 39) SS BOND : angle 1.36096 ( 78) covalent geometry : bond 0.00215 (25208) covalent geometry : angle 0.54207 (34293) *********************** 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 75 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 40 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8696 (m-80) cc_final: 0.8476 (m-80) REVERT: B 421 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.4688 (t80) REVERT: B 454 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7057 (ttt90) REVERT: B 752 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8589 (tt) REVERT: C 369 TYR cc_start: 0.7395 (t80) cc_final: 0.6919 (m-80) REVERT: C 494 SER cc_start: 0.6417 (OUTLIER) cc_final: 0.6209 (t) outliers start: 35 outliers final: 19 residues processed: 73 average time/residue: 0.3726 time to fit residues: 45.4410 Evaluate side-chains 58 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 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 B residue 143 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 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 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 494 SER 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 192 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.051782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037733 restraints weight = 164535.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038782 restraints weight = 83522.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039447 restraints weight = 55229.995| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25308 Z= 0.178 Angle : 0.589 9.659 34554 Z= 0.303 Chirality : 0.044 0.195 4086 Planarity : 0.004 0.061 4353 Dihedral : 6.010 58.173 4558 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 1.39 % Allowed : 6.83 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3003 helix: 2.01 (0.21), residues: 675 sheet: 0.13 (0.19), residues: 639 loop : -0.60 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.005 0.001 HIS B1064 PHE 0.019 0.001 PHE B 456 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 47) link_NAG-ASN : angle 2.23060 ( 141) link_BETA1-4 : bond 0.00350 ( 14) link_BETA1-4 : angle 1.81192 ( 42) hydrogen bonds : bond 0.04142 ( 1021) hydrogen bonds : angle 5.48954 ( 2841) SS BOND : bond 0.00422 ( 39) SS BOND : angle 1.27697 ( 78) covalent geometry : bond 0.00413 (25208) covalent geometry : angle 0.56740 (34293) *********************** 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 71 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 34 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8715 (m-80) cc_final: 0.8488 (m-80) REVERT: B 421 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.5127 (t80) REVERT: B 752 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8587 (tt) REVERT: C 369 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7035 (m-80) outliers start: 37 outliers final: 23 residues processed: 69 average time/residue: 0.3200 time to fit residues: 40.0337 Evaluate side-chains 59 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 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 738 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 292 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 226 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.051133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.037032 restraints weight = 164305.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038054 restraints weight = 84210.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038699 restraints weight = 56198.798| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25308 Z= 0.243 Angle : 0.644 8.736 34554 Z= 0.329 Chirality : 0.046 0.209 4086 Planarity : 0.004 0.059 4353 Dihedral : 6.317 58.773 4558 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 1.50 % Allowed : 7.47 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3003 helix: 1.74 (0.21), residues: 680 sheet: -0.01 (0.19), residues: 634 loop : -0.71 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE B 543 TYR 0.020 0.002 TYR C1067 ARG 0.005 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 47) link_NAG-ASN : angle 2.24563 ( 141) link_BETA1-4 : bond 0.00364 ( 14) link_BETA1-4 : angle 1.89219 ( 42) hydrogen bonds : bond 0.04556 ( 1021) hydrogen bonds : angle 5.70072 ( 2841) SS BOND : bond 0.00497 ( 39) SS BOND : angle 1.49745 ( 78) covalent geometry : bond 0.00566 (25208) covalent geometry : angle 0.62270 (34293) *********************** 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 74 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 34 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8869 (pp) REVERT: A 473 TYR cc_start: 0.8718 (m-80) cc_final: 0.8474 (m-80) REVERT: B 421 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.5037 (t80) REVERT: B 752 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8602 (tt) REVERT: C 369 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7130 (m-80) outliers start: 40 outliers final: 28 residues processed: 72 average time/residue: 0.3201 time to fit residues: 41.7885 Evaluate side-chains 63 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP 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 421 TYR 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 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 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 88 ASP 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 472 ILE Chi-restraints excluded: chain C residue 538 CYS 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 80 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.051362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037295 restraints weight = 163719.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038349 restraints weight = 82246.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038988 restraints weight = 54247.873| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25308 Z= 0.177 Angle : 0.580 7.949 34554 Z= 0.298 Chirality : 0.044 0.228 4086 Planarity : 0.004 0.059 4353 Dihedral : 6.084 58.273 4556 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 1.35 % Allowed : 8.15 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3003 helix: 1.93 (0.21), residues: 674 sheet: 0.09 (0.19), residues: 640 loop : -0.70 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS B1064 PHE 0.019 0.001 PHE B 456 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 47) link_NAG-ASN : angle 2.06516 ( 141) link_BETA1-4 : bond 0.00367 ( 14) link_BETA1-4 : angle 1.72939 ( 42) hydrogen bonds : bond 0.04178 ( 1021) hydrogen bonds : angle 5.53749 ( 2841) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.34829 ( 78) covalent geometry : bond 0.00409 (25208) covalent geometry : angle 0.55977 (34293) *********************** 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 68 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 32 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 473 TYR cc_start: 0.8752 (m-80) cc_final: 0.8503 (m-80) REVERT: B 421 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5097 (t80) REVERT: B 454 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7271 (ttt180) REVERT: B 752 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8583 (tt) REVERT: B 786 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7854 (pmtt) REVERT: C 369 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7140 (m-80) outliers start: 36 outliers final: 26 residues processed: 66 average time/residue: 0.3380 time to fit residues: 39.6675 Evaluate side-chains 63 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 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 1104 VAL Chi-restraints excluded: chain B residue 318 PHE 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 786 LYS 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 369 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 489 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 247 optimal weight: 9.9990 chunk 264 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.050885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036794 restraints weight = 165320.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037818 restraints weight = 83625.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038468 restraints weight = 55744.321| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25308 Z= 0.253 Angle : 0.638 8.370 34554 Z= 0.326 Chirality : 0.046 0.213 4086 Planarity : 0.004 0.059 4353 Dihedral : 6.240 58.475 4556 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 1.61 % Allowed : 8.33 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3003 helix: 1.78 (0.21), residues: 674 sheet: -0.04 (0.19), residues: 637 loop : -0.78 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE B 543 TYR 0.019 0.002 TYR C1067 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 47) link_NAG-ASN : angle 2.12617 ( 141) link_BETA1-4 : bond 0.00367 ( 14) link_BETA1-4 : angle 1.89497 ( 42) hydrogen bonds : bond 0.04518 ( 1021) hydrogen bonds : angle 5.70747 ( 2841) SS BOND : bond 0.00478 ( 39) SS BOND : angle 1.38492 ( 78) covalent geometry : bond 0.00588 (25208) covalent geometry : angle 0.61878 (34293) *********************** 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 74 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 31 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 473 TYR cc_start: 0.8722 (m-80) cc_final: 0.8480 (m-80) REVERT: B 421 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.5324 (t80) REVERT: B 752 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8607 (tt) REVERT: B 786 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7839 (pmtt) REVERT: C 369 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7165 (m-80) outliers start: 43 outliers final: 34 residues processed: 72 average time/residue: 0.3167 time to fit residues: 41.6756 Evaluate side-chains 70 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 31 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 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 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP 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 391 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 489 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 167 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 154 optimal weight: 0.0870 chunk 216 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 301 optimal weight: 3.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.051690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037831 restraints weight = 164665.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038884 restraints weight = 82562.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.039539 restraints weight = 54364.251| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25308 Z= 0.118 Angle : 0.540 11.167 34554 Z= 0.278 Chirality : 0.044 0.300 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.765 58.048 4556 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.31 % Allowed : 8.67 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3003 helix: 2.19 (0.21), residues: 670 sheet: 0.22 (0.20), residues: 623 loop : -0.70 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.003 0.001 HIS C 655 PHE 0.018 0.001 PHE B 456 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 47) link_NAG-ASN : angle 1.82643 ( 141) link_BETA1-4 : bond 0.00436 ( 14) link_BETA1-4 : angle 1.51359 ( 42) hydrogen bonds : bond 0.03737 ( 1021) hydrogen bonds : angle 5.32068 ( 2841) SS BOND : bond 0.00558 ( 39) SS BOND : angle 1.39820 ( 78) covalent geometry : bond 0.00267 (25208) covalent geometry : angle 0.52195 (34293) *********************** 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: 35 poor density : 34 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8728 (pp) REVERT: A 473 TYR cc_start: 0.8723 (m-80) cc_final: 0.8495 (m-80) REVERT: B 421 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5098 (t80) REVERT: B 454 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7334 (ttt180) REVERT: B 752 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 369 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7133 (m-80) outliers start: 35 outliers final: 27 residues processed: 67 average time/residue: 0.3280 time to fit residues: 38.9047 Evaluate side-chains 63 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU 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 391 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 171 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 76 optimal weight: 0.1980 chunk 292 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037989 restraints weight = 163925.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039047 restraints weight = 82230.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039689 restraints weight = 54168.327| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25308 Z= 0.115 Angle : 0.534 11.044 34554 Z= 0.275 Chirality : 0.043 0.243 4086 Planarity : 0.004 0.059 4353 Dihedral : 5.517 57.823 4556 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 1.24 % Allowed : 8.90 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3003 helix: 2.32 (0.21), residues: 671 sheet: 0.24 (0.19), residues: 641 loop : -0.65 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 PHE 0.017 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 47) link_NAG-ASN : angle 1.74808 ( 141) link_BETA1-4 : bond 0.00364 ( 14) link_BETA1-4 : angle 1.51448 ( 42) hydrogen bonds : bond 0.03677 ( 1021) hydrogen bonds : angle 5.24856 ( 2841) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.77742 ( 78) covalent geometry : bond 0.00261 (25208) covalent geometry : angle 0.51470 (34293) ********************** 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 64 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 473 TYR cc_start: 0.8707 (m-80) cc_final: 0.8481 (m-80) REVERT: B 323 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9215 (p) REVERT: B 421 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.4823 (t80) REVERT: B 454 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7408 (ttt180) REVERT: B 752 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8594 (tt) REVERT: C 369 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.7117 (m-80) outliers start: 33 outliers final: 27 residues processed: 62 average time/residue: 0.3236 time to fit residues: 36.8385 Evaluate side-chains 64 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 155 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 130 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.038035 restraints weight = 163663.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039086 restraints weight = 82381.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039720 restraints weight = 54193.769| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25308 Z= 0.121 Angle : 0.521 9.082 34554 Z= 0.268 Chirality : 0.043 0.230 4086 Planarity : 0.004 0.056 4353 Dihedral : 5.281 57.387 4556 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % Rotamer: Outliers : 1.35 % Allowed : 8.86 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3003 helix: 2.36 (0.21), residues: 671 sheet: 0.28 (0.20), residues: 635 loop : -0.60 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 PHE 0.017 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 47) link_NAG-ASN : angle 1.64769 ( 141) link_BETA1-4 : bond 0.00355 ( 14) link_BETA1-4 : angle 1.48789 ( 42) hydrogen bonds : bond 0.03618 ( 1021) hydrogen bonds : angle 5.17060 ( 2841) SS BOND : bond 0.00379 ( 39) SS BOND : angle 1.50362 ( 78) covalent geometry : bond 0.00278 (25208) covalent geometry : angle 0.50399 (34293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7191.46 seconds wall clock time: 126 minutes 9.17 seconds (7569.17 seconds total)