Starting phenix.real_space_refine on Sun Jun 22 20:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy3_60554/06_2025/8zy3_60554.cif" } resolution = 3.3 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= 0.000 sd= 0.007 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 123 5.16 5 C 16713 2.51 5 N 4290 2.21 5 O 5169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8485 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1039} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8485 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1039} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8485 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1039} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 15.66, per 1000 atoms: 0.60 Number of scatterers: 26295 At special positions: 0 Unit cell: (134.64, 146.52, 166.32, 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 123 16.00 O 5169 8.00 N 4290 7.00 C 16713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 165 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 752 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 741 " distance=2.02 Simple disulfide: pdb=" SG CYS A 832 " - pdb=" SG CYS A 843 " distance=2.03 Simple disulfide: pdb=" SG CYS A1024 " - pdb=" SG CYS A1035 " distance=2.03 Simple disulfide: pdb=" SG CYS A1074 " - pdb=" SG CYS A1118 " distance=2.04 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.02 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 741 " distance=2.02 Simple disulfide: pdb=" SG CYS B 832 " - pdb=" SG CYS B 843 " distance=2.03 Simple disulfide: pdb=" SG CYS B1024 " - pdb=" SG CYS B1035 " distance=2.02 Simple disulfide: pdb=" SG CYS B1074 " - pdb=" SG CYS B1118 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 165 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.04 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 730 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 741 " distance=2.02 Simple disulfide: pdb=" SG CYS C 832 " - pdb=" SG CYS C 843 " distance=2.03 Simple disulfide: pdb=" SG CYS C1024 " - pdb=" SG CYS C1035 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1118 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 18 " " NAG A1302 " - " ASN A 31 " " NAG A1303 " - " ASN A 62 " " NAG A1304 " - " ASN A 164 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A 278 " " NAG A1307 " - " ASN A 327 " " NAG A1308 " - " ASN A 339 " " NAG A1309 " - " ASN A 366 " " NAG A1310 " - " ASN A 612 " " NAG A1311 " - " ASN A 653 " " NAG A1312 " - " ASN A 701 " " NAG A1313 " - " ASN A 709 " " NAG A1314 " - " ASN A1066 " " NAG A1315 " - " ASN A1090 " " NAG A1316 " - " ASN A1126 " " NAG B1301 " - " ASN B 18 " " NAG B1302 " - " ASN B 31 " " NAG B1303 " - " ASN B 62 " " NAG B1304 " - " ASN B 164 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 278 " " NAG B1307 " - " ASN B 327 " " NAG B1309 " - " ASN B 366 " " NAG B1310 " - " ASN B 612 " " NAG B1311 " - " ASN B 653 " " NAG B1312 " - " ASN B 701 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B1066 " " NAG B1315 " - " ASN B1090 " " NAG B1316 " - " ASN B1126 " " NAG C1301 " - " ASN C 18 " " NAG C1302 " - " ASN C 31 " " NAG C1303 " - " ASN C 62 " " NAG C1304 " - " ASN C 164 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 278 " " NAG C1307 " - " ASN C 327 " " NAG C1308 " - " ASN C 339 " " NAG C1309 " - " ASN C 366 " " NAG C1310 " - " ASN C 612 " " NAG C1311 " - " ASN C 653 " " NAG C1312 " - " ASN C 701 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1066 " " NAG C1315 " - " ASN C1090 " " NAG C1316 " - " ASN C1126 " " NAG D 1 " - " ASN A 793 " " NAG E 1 " - " ASN A 233 " " NAG F 1 " - " ASN B 793 " " NAG G 1 " - " ASN B 233 " " NAG H 1 " - " ASN C 793 " " NAG I 1 " - " ASN C 233 " Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 3.5 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 51 sheets defined 24.6% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.651A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.823A pdb=" N TRP A 349 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 4.124A pdb=" N VAL A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.591A pdb=" N LEU A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.484A pdb=" N ARG A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.719A pdb=" N GLY A 478 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 622 through 625 removed outlier: 3.568A pdb=" N LEU A 625 " --> pdb=" O ALA A 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.920A pdb=" N GLN A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 775 removed outlier: 3.548A pdb=" N GLY A 761 " --> pdb=" O ARG A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 858 through 876 removed outlier: 3.555A pdb=" N GLN A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 Processing helix chain 'A' and resid 889 through 902 Processing helix chain 'A' and resid 905 through 910 removed outlier: 3.731A pdb=" N TYR A 909 " --> pdb=" O GLN A 905 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 905 through 910' Processing helix chain 'A' and resid 911 through 929 removed outlier: 4.271A pdb=" N ALA A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 957 removed outlier: 4.746A pdb=" N VAL A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.501A pdb=" N ILE A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 1024 removed outlier: 3.545A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.623A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.858A pdb=" N VAL B 363 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.640A pdb=" N LEU B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 384' Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.521A pdb=" N ARG B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.910A pdb=" N GLY B 478 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 747 through 749 No H-bonds generated for 'chain 'B' and resid 747 through 749' Processing helix chain 'B' and resid 752 through 775 removed outlier: 3.570A pdb=" N ALA B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 840 through 847 Processing helix chain 'B' and resid 858 through 876 Processing helix chain 'B' and resid 878 through 882 Processing helix chain 'B' and resid 889 through 902 Processing helix chain 'B' and resid 905 through 910 removed outlier: 3.737A pdb=" N TYR B 909 " --> pdb=" O GLN B 905 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B 910 " --> pdb=" O ASN B 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 905 through 910' Processing helix chain 'B' and resid 911 through 929 removed outlier: 4.260A pdb=" N ALA B 922 " --> pdb=" O GLN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 957 removed outlier: 4.697A pdb=" N VAL B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 950 " --> pdb=" O GLN B 946 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 951 " --> pdb=" O ASN B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 976 Processing helix chain 'B' and resid 977 through 1025 removed outlier: 3.502A pdb=" N GLU B 982 " --> pdb=" O LYS B 978 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 983 " --> pdb=" O VAL B 979 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN B 984 " --> pdb=" O GLU B 980 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 360 through 365 removed outlier: 3.891A pdb=" N VAL C 363 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 386 removed outlier: 3.639A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.556A pdb=" N ARG C 404 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.755A pdb=" N GLY C 478 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 622 through 625 removed outlier: 3.554A pdb=" N LEU C 625 " --> pdb=" O ALA C 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 625' Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 738 through 747 removed outlier: 3.682A pdb=" N GLN C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 775 Processing helix chain 'C' and resid 808 through 818 Processing helix chain 'C' and resid 840 through 847 Processing helix chain 'C' and resid 858 through 876 Processing helix chain 'C' and resid 878 through 882 Processing helix chain 'C' and resid 889 through 902 Processing helix chain 'C' and resid 905 through 910 removed outlier: 3.618A pdb=" N TYR C 909 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 929 removed outlier: 4.168A pdb=" N ALA C 922 " --> pdb=" O GLN C 918 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 957 removed outlier: 4.737A pdb=" N VAL C 943 " --> pdb=" O LYS C 939 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN C 949 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 950 " --> pdb=" O GLN C 946 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 952 " --> pdb=" O ALA C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 976 removed outlier: 3.532A pdb=" N ILE C 972 " --> pdb=" O VAL C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 1024 removed outlier: 3.513A pdb=" N GLU C 982 " --> pdb=" O LYS C 978 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL C 983 " --> pdb=" O VAL C 979 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN C 984 " --> pdb=" O GLU C 980 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.462A pdb=" N ASN A 62 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR A 265 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 259 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 187 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER A 204 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N TYR A 206 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N LEU A 222 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 37 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 56 removed outlier: 4.017A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.000A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 242 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 101 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 130 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 324 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.822A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.298A pdb=" N GLU A 650 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR A 688 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 694 removed outlier: 6.564A pdb=" N ALA A 693 " --> pdb=" O ILE B 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 707 removed outlier: 3.624A pdb=" N ALA A1070 " --> pdb=" O PHE A1087 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A1087 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 710 through 720 removed outlier: 6.954A pdb=" N GLY A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER A1047 " --> pdb=" O GLY A1051 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1053 " --> pdb=" O PRO A1045 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A1055 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A1043 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A1057 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 727 removed outlier: 4.245A pdb=" N LYS A 725 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB9, first strand: chain 'A' and resid 1112 through 1117 removed outlier: 4.548A pdb=" N ALA A1079 " --> pdb=" O SER A1115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.281A pdb=" N ASN B 62 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N TYR B 265 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 96 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR B 187 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 202 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 226 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER B 204 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N TYR B 206 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N LEU B 222 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 37 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 56 removed outlier: 6.447A pdb=" N MET B 272 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 284 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS B 274 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 242 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 101 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AC6, first strand: chain 'B' and resid 320 through 324 Processing sheet with id=AC7, first strand: chain 'B' and resid 350 through 353 Processing sheet with id=AC8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.397A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AD1, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AD2, first strand: chain 'B' and resid 561 through 562 Processing sheet with id=AD3, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.386A pdb=" N GLU B 650 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR B 688 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 694 removed outlier: 6.612A pdb=" N ALA B 693 " --> pdb=" O ILE C 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 703 through 707 removed outlier: 3.523A pdb=" N ALA B1070 " --> pdb=" O PHE B1087 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B1087 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 710 through 720 removed outlier: 6.935A pdb=" N GLY B1051 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER B1047 " --> pdb=" O GLY B1051 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B1053 " --> pdb=" O PRO B1045 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B1055 " --> pdb=" O SER B1043 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER B1043 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B1057 " --> pdb=" O LEU B1041 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 725 through 728 removed outlier: 4.286A pdb=" N LYS B 725 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1112 through 1117 removed outlier: 3.653A pdb=" N SER B1115 " --> pdb=" O ALA B1079 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B1079 " --> pdb=" O SER B1115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.773A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASN C 62 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR C 265 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU C 96 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR C 187 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER C 204 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N TYR C 206 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU C 222 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C 37 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 56 removed outlier: 6.493A pdb=" N MET C 272 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C 284 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS C 274 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.772A pdb=" N LEU C 141 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.824A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR C 242 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 101 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AE5, first strand: chain 'C' and resid 320 through 324 removed outlier: 3.610A pdb=" N PHE C 539 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 350 through 353 removed outlier: 3.540A pdb=" N ASN C 350 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.840A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AE9, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AF1, first strand: chain 'C' and resid 561 through 562 Processing sheet with id=AF2, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.357A pdb=" N GLU C 650 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N THR C 688 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 666 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 703 through 707 removed outlier: 4.308A pdb=" N PHE C1087 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 710 through 720 removed outlier: 6.940A pdb=" N GLY C1051 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER C1047 " --> pdb=" O GLY C1051 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1053 " --> pdb=" O PRO C1045 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1055 " --> pdb=" O SER C1043 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C1043 " --> pdb=" O LEU C1055 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C1057 " --> pdb=" O LEU C1041 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 725 through 728 removed outlier: 4.339A pdb=" N LYS C 725 " --> pdb=" O LEU C 853 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1112 through 1117 removed outlier: 3.526A pdb=" N SER C1115 " --> pdb=" O ALA C1079 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C1079 " --> pdb=" O SER C1115 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2613 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: 13.28 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8308 1.34 - 1.46: 6462 1.46 - 1.58: 11951 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 26877 Sorted by residual: bond pdb=" N ILE B 43 " pdb=" CA ILE B 43 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.48e+01 bond pdb=" N ILE A 232 " pdb=" CA ILE A 232 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ASP B 41 " pdb=" CA ASP B 41 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" N LEU C 69 " pdb=" CA LEU C 69 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.18e-02 7.18e+03 7.49e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.02e+00 ... (remaining 26872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 34982 1.67 - 3.35: 1372 3.35 - 5.02: 157 5.02 - 6.69: 39 6.69 - 8.36: 29 Bond angle restraints: 36579 Sorted by residual: angle pdb=" N ILE B 43 " pdb=" CA ILE B 43 " pdb=" C ILE B 43 " ideal model delta sigma weight residual 113.53 107.62 5.91 9.80e-01 1.04e+00 3.64e+01 angle pdb=" N ILE A 43 " pdb=" CA ILE A 43 " pdb=" C ILE A 43 " ideal model delta sigma weight residual 113.53 109.13 4.40 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C ASN C 251 " pdb=" CA ASN C 251 " pdb=" CB ASN C 251 " ideal model delta sigma weight residual 116.63 111.52 5.11 1.16e+00 7.43e-01 1.94e+01 angle pdb=" C CYS B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C LYS C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta sigma weight residual 122.46 128.11 -5.65 1.41e+00 5.03e-01 1.61e+01 ... (remaining 36574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15204 17.99 - 35.98: 1239 35.98 - 53.97: 234 53.97 - 71.96: 57 71.96 - 89.94: 27 Dihedral angle restraints: 16761 sinusoidal: 7236 harmonic: 9525 Sorted by residual: dihedral pdb=" CB CYS A 613 " pdb=" SG CYS A 613 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual -86.00 -170.26 84.26 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS C1074 " pdb=" SG CYS C1074 " pdb=" SG CYS C1118 " pdb=" CB CYS C1118 " ideal model delta sinusoidal sigma weight residual -86.00 -5.06 -80.94 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 658 " pdb=" SG CYS A 658 " pdb=" SG CYS A 667 " pdb=" CB CYS A 667 " ideal model delta sinusoidal sigma weight residual -86.00 -7.41 -78.59 1 1.00e+01 1.00e-02 7.70e+01 ... (remaining 16758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4000 0.097 - 0.194: 289 0.194 - 0.291: 13 0.291 - 0.388: 13 0.388 - 0.485: 1 Chirality restraints: 4316 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 612 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C2 NAG G 2 " pdb=" C1 NAG G 2 " pdb=" C3 NAG G 2 " pdb=" N2 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 4313 not shown) Planarity restraints: 4706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 65 " -0.030 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP A 65 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 65 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 65 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 65 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 65 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 65 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 65 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 65 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 65 " -0.016 2.00e-02 2.50e+03 1.93e-02 9.33e+00 pdb=" CG TRP C 65 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 65 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 65 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 65 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 65 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 65 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 65 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 65 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 65 " -0.018 2.00e-02 2.50e+03 1.61e-02 6.46e+00 pdb=" CG TRP B 65 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 65 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 65 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 65 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 65 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 65 " 0.000 2.00e-02 2.50e+03 ... (remaining 4703 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6356 2.79 - 3.32: 22828 3.32 - 3.84: 42857 3.84 - 4.37: 49935 4.37 - 4.90: 87747 Nonbonded interactions: 209723 Sorted by model distance: nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 261 " model vdw 2.262 3.040 nonbonded pdb=" O ALA C 871 " pdb=" OG1 THR C 875 " model vdw 2.265 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 261 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN B 957 " pdb=" OG SER B 995 " model vdw 2.288 3.040 nonbonded pdb=" O ALA A 871 " pdb=" OG1 THR A 875 " model vdw 2.290 3.040 ... (remaining 209718 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.150 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 63.880 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26978 Z= 0.236 Angle : 0.796 10.862 36840 Z= 0.408 Chirality : 0.055 0.485 4316 Planarity : 0.005 0.057 4653 Dihedral : 13.578 89.944 10527 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.90 (0.13), residues: 3240 helix: -0.99 (0.18), residues: 726 sheet: -0.33 (0.19), residues: 714 loop : -1.80 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 65 HIS 0.004 0.001 HIS B 621 PHE 0.025 0.002 PHE C 237 TYR 0.035 0.002 TYR C1130 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 53) link_NAG-ASN : angle 3.37307 ( 159) link_BETA1-4 : bond 0.00739 ( 6) link_BETA1-4 : angle 5.33583 ( 18) hydrogen bonds : bond 0.16620 ( 969) hydrogen bonds : angle 8.04234 ( 2613) SS BOND : bond 0.00513 ( 42) SS BOND : angle 2.01847 ( 84) covalent geometry : bond 0.00500 (26877) covalent geometry : angle 0.75215 (36579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.746 Fit side-chains revert: symmetry clash REVERT: A 894 MET cc_start: 0.8569 (mmt) cc_final: 0.8205 (mmt) REVERT: C 732 MET cc_start: 0.8418 (mtm) cc_final: 0.8046 (mtm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3392 time to fit residues: 55.1363 Evaluate side-chains 64 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.0070 chunk 247 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 609 GLN ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN C 540 ASN C 560 GLN C 893 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.063550 restraints weight = 55922.810| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.51 r_work: 0.2730 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26978 Z= 0.145 Angle : 0.622 9.850 36840 Z= 0.303 Chirality : 0.047 0.327 4316 Planarity : 0.004 0.037 4653 Dihedral : 8.305 59.652 4788 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.46 % Allowed : 4.03 % Favored : 95.51 % 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: -1.43 (0.14), residues: 3240 helix: -0.08 (0.20), residues: 729 sheet: -0.39 (0.18), residues: 723 loop : -1.58 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 254 HIS 0.005 0.001 HIS C1040 PHE 0.015 0.001 PHE C 237 TYR 0.018 0.001 TYR B1130 ARG 0.004 0.000 ARG B 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 53) link_NAG-ASN : angle 2.60058 ( 159) link_BETA1-4 : bond 0.00329 ( 6) link_BETA1-4 : angle 3.64257 ( 18) hydrogen bonds : bond 0.04237 ( 969) hydrogen bonds : angle 5.91101 ( 2613) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.65565 ( 84) covalent geometry : bond 0.00332 (26877) covalent geometry : angle 0.58928 (36579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 3.105 Fit side-chains REVERT: B 175 MET cc_start: 0.3613 (pmm) cc_final: 0.3253 (pmm) REVERT: C 65 TRP cc_start: 0.8755 (OUTLIER) cc_final: 0.8409 (t60) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.3427 time to fit residues: 51.2847 Evaluate side-chains 72 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 202 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 190 optimal weight: 0.0070 chunk 42 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 560 GLN ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN C 125 ASN C 609 GLN C 917 ASN C 947 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.061986 restraints weight = 55881.437| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.51 r_work: 0.2693 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26978 Z= 0.181 Angle : 0.625 9.682 36840 Z= 0.302 Chirality : 0.047 0.287 4316 Planarity : 0.003 0.035 4653 Dihedral : 7.645 59.112 4788 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.57 % Allowed : 6.89 % Favored : 92.54 % 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: -1.22 (0.14), residues: 3240 helix: 0.36 (0.20), residues: 711 sheet: -0.37 (0.18), residues: 723 loop : -1.50 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 254 HIS 0.006 0.001 HIS C1040 PHE 0.015 0.001 PHE A 44 TYR 0.018 0.001 TYR B1059 ARG 0.005 0.000 ARG C 236 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 53) link_NAG-ASN : angle 2.63166 ( 159) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 3.58702 ( 18) hydrogen bonds : bond 0.04125 ( 969) hydrogen bonds : angle 5.56003 ( 2613) SS BOND : bond 0.00494 ( 42) SS BOND : angle 1.75484 ( 84) covalent geometry : bond 0.00430 (26877) covalent geometry : angle 0.59113 (36579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 3.077 Fit side-chains REVERT: A 249 MET cc_start: 0.6511 (mpp) cc_final: 0.5674 (ptp) REVERT: B 254 TRP cc_start: 0.7343 (p90) cc_final: 0.6526 (p90) REVERT: B 732 MET cc_start: 0.9196 (mmm) cc_final: 0.8894 (mmm) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.3325 time to fit residues: 46.3655 Evaluate side-chains 67 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 201 optimal weight: 4.9990 chunk 165 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 315 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.062718 restraints weight = 56117.196| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.53 r_work: 0.2703 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26978 Z= 0.138 Angle : 0.586 9.610 36840 Z= 0.282 Chirality : 0.046 0.275 4316 Planarity : 0.003 0.034 4653 Dihedral : 7.181 59.102 4788 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.88 % Allowed : 8.13 % Favored : 90.99 % 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: -0.99 (0.14), residues: 3240 helix: 0.64 (0.20), residues: 732 sheet: -0.25 (0.19), residues: 726 loop : -1.42 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 254 HIS 0.004 0.001 HIS A1040 PHE 0.015 0.001 PHE B 29 TYR 0.016 0.001 TYR B1059 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 53) link_NAG-ASN : angle 2.45742 ( 159) link_BETA1-4 : bond 0.00454 ( 6) link_BETA1-4 : angle 3.47382 ( 18) hydrogen bonds : bond 0.03628 ( 969) hydrogen bonds : angle 5.33050 ( 2613) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.56355 ( 84) covalent geometry : bond 0.00320 (26877) covalent geometry : angle 0.55455 (36579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 2.898 Fit side-chains REVERT: A 175 MET cc_start: 0.2571 (pmm) cc_final: 0.2269 (pmm) REVERT: A 249 MET cc_start: 0.6719 (mpp) cc_final: 0.5313 (ptp) REVERT: B 254 TRP cc_start: 0.7403 (p90) cc_final: 0.6637 (p90) REVERT: B 732 MET cc_start: 0.9171 (mmm) cc_final: 0.8904 (mmm) outliers start: 25 outliers final: 15 residues processed: 90 average time/residue: 0.3232 time to fit residues: 53.1117 Evaluate side-chains 74 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 103 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 51 optimal weight: 0.0370 chunk 193 optimal weight: 6.9990 chunk 138 optimal weight: 0.4980 chunk 324 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.064410 restraints weight = 55868.942| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.53 r_work: 0.2743 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26978 Z= 0.094 Angle : 0.554 9.635 36840 Z= 0.265 Chirality : 0.045 0.282 4316 Planarity : 0.003 0.037 4653 Dihedral : 6.797 59.081 4788 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.95 % Allowed : 9.37 % Favored : 89.68 % 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: -0.79 (0.14), residues: 3240 helix: 1.26 (0.21), residues: 672 sheet: -0.23 (0.19), residues: 732 loop : -1.37 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 254 HIS 0.003 0.000 HIS A1040 PHE 0.013 0.001 PHE B 29 TYR 0.019 0.001 TYR C1130 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 53) link_NAG-ASN : angle 2.27045 ( 159) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 3.45547 ( 18) hydrogen bonds : bond 0.03258 ( 969) hydrogen bonds : angle 5.13052 ( 2613) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.33342 ( 84) covalent geometry : bond 0.00205 (26877) covalent geometry : angle 0.52625 (36579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 3.776 Fit side-chains REVERT: A 249 MET cc_start: 0.6446 (mpp) cc_final: 0.5447 (ptp) REVERT: B 254 TRP cc_start: 0.7356 (p90) cc_final: 0.6666 (p90) REVERT: C 118 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8732 (tp) outliers start: 27 outliers final: 11 residues processed: 88 average time/residue: 0.5059 time to fit residues: 81.7392 Evaluate side-chains 71 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 174 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 109 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS A 609 GLN ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.059876 restraints weight = 57038.843| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.65 r_work: 0.2641 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26978 Z= 0.202 Angle : 0.627 9.723 36840 Z= 0.301 Chirality : 0.047 0.272 4316 Planarity : 0.003 0.041 4653 Dihedral : 6.950 59.139 4788 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.34 % Allowed : 10.14 % Favored : 88.51 % 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: -0.81 (0.14), residues: 3240 helix: 0.91 (0.20), residues: 732 sheet: -0.13 (0.18), residues: 738 loop : -1.37 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 254 HIS 0.005 0.001 HIS B1040 PHE 0.020 0.002 PHE B 29 TYR 0.017 0.001 TYR B1059 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 53) link_NAG-ASN : angle 2.55703 ( 159) link_BETA1-4 : bond 0.00395 ( 6) link_BETA1-4 : angle 3.45144 ( 18) hydrogen bonds : bond 0.03937 ( 969) hydrogen bonds : angle 5.29599 ( 2613) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.76935 ( 84) covalent geometry : bond 0.00484 (26877) covalent geometry : angle 0.59497 (36579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 2.950 Fit side-chains REVERT: A 249 MET cc_start: 0.6610 (mpp) cc_final: 0.5519 (ptp) REVERT: B 254 TRP cc_start: 0.7574 (p90) cc_final: 0.6951 (p90) REVERT: C 118 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8724 (tp) outliers start: 38 outliers final: 26 residues processed: 94 average time/residue: 0.4282 time to fit residues: 71.9661 Evaluate side-chains 82 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 0.6980 chunk 314 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 168 optimal weight: 0.0470 chunk 251 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 287 optimal weight: 0.6980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN ** C 947 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 = 0.3221 r_free = 0.3221 target = 0.081351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061805 restraints weight = 57043.479| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.67 r_work: 0.2688 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26978 Z= 0.103 Angle : 0.565 9.571 36840 Z= 0.270 Chirality : 0.045 0.283 4316 Planarity : 0.003 0.041 4653 Dihedral : 6.700 59.562 4788 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.17 % Allowed : 10.68 % Favored : 88.16 % 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: -0.66 (0.14), residues: 3240 helix: 1.33 (0.21), residues: 687 sheet: -0.09 (0.19), residues: 738 loop : -1.33 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 254 HIS 0.003 0.001 HIS A1040 PHE 0.014 0.001 PHE B 29 TYR 0.018 0.001 TYR C1130 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 53) link_NAG-ASN : angle 2.32600 ( 159) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 3.44144 ( 18) hydrogen bonds : bond 0.03372 ( 969) hydrogen bonds : angle 5.10792 ( 2613) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.57615 ( 84) covalent geometry : bond 0.00231 (26877) covalent geometry : angle 0.53519 (36579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 2.949 Fit side-chains REVERT: A 249 MET cc_start: 0.6537 (mpp) cc_final: 0.4996 (ptp) REVERT: B 249 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3081 (ppp) REVERT: C 118 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8710 (tp) outliers start: 33 outliers final: 23 residues processed: 92 average time/residue: 0.3289 time to fit residues: 54.5559 Evaluate side-chains 83 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 307 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 262 optimal weight: 0.0980 chunk 229 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 195 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN ** C 947 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 = 0.3233 r_free = 0.3233 target = 0.081973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062900 restraints weight = 56225.177| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.59 r_work: 0.2717 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26978 Z= 0.097 Angle : 0.552 9.618 36840 Z= 0.263 Chirality : 0.045 0.279 4316 Planarity : 0.003 0.040 4653 Dihedral : 6.542 59.223 4788 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.10 % Allowed : 10.85 % Favored : 88.05 % 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: -0.59 (0.15), residues: 3240 helix: 1.57 (0.21), residues: 672 sheet: -0.14 (0.18), residues: 747 loop : -1.30 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP C 254 HIS 0.003 0.000 HIS B1040 PHE 0.014 0.001 PHE B 29 TYR 0.015 0.001 TYR B1130 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 53) link_NAG-ASN : angle 2.21452 ( 159) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 3.42849 ( 18) hydrogen bonds : bond 0.03190 ( 969) hydrogen bonds : angle 4.99374 ( 2613) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.36947 ( 84) covalent geometry : bond 0.00219 (26877) covalent geometry : angle 0.52491 (36579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 2.728 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.6541 (mpp) cc_final: 0.4921 (ptp) REVERT: B 249 MET cc_start: 0.4113 (OUTLIER) cc_final: 0.2959 (ppp) REVERT: C 118 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8743 (tp) outliers start: 31 outliers final: 22 residues processed: 91 average time/residue: 0.3191 time to fit residues: 51.8807 Evaluate side-chains 87 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 125 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 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 = 0.3166 r_free = 0.3166 target = 0.078430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.058891 restraints weight = 57381.355| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.64 r_work: 0.2622 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 26978 Z= 0.252 Angle : 0.653 9.739 36840 Z= 0.315 Chirality : 0.048 0.277 4316 Planarity : 0.004 0.042 4653 Dihedral : 6.905 59.083 4788 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.10 % Allowed : 11.03 % Favored : 87.88 % 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: -0.77 (0.14), residues: 3240 helix: 1.01 (0.21), residues: 729 sheet: -0.11 (0.18), residues: 738 loop : -1.37 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 254 HIS 0.007 0.001 HIS B1040 PHE 0.021 0.002 PHE B 86 TYR 0.020 0.002 TYR B1059 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 53) link_NAG-ASN : angle 2.61053 ( 159) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 3.45787 ( 18) hydrogen bonds : bond 0.04131 ( 969) hydrogen bonds : angle 5.29481 ( 2613) SS BOND : bond 0.00595 ( 42) SS BOND : angle 1.95553 ( 84) covalent geometry : bond 0.00596 (26877) covalent geometry : angle 0.62053 (36579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 2.758 Fit side-chains REVERT: A 249 MET cc_start: 0.6543 (mpp) cc_final: 0.4953 (ptp) REVERT: A 894 MET cc_start: 0.9162 (tpp) cc_final: 0.8749 (mmt) REVERT: B 249 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3040 (ppp) REVERT: B 732 MET cc_start: 0.9255 (mmm) cc_final: 0.8861 (mtp) REVERT: C 118 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8763 (tp) REVERT: C 188 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9083 (tt) REVERT: C 254 TRP cc_start: 0.7788 (p-90) cc_final: 0.7567 (p-90) outliers start: 31 outliers final: 21 residues processed: 84 average time/residue: 0.3163 time to fit residues: 47.9114 Evaluate side-chains 80 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1042 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 289 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 273 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 272 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 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 = 0.3209 r_free = 0.3209 target = 0.080679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.061547 restraints weight = 56455.716| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.60 r_work: 0.2683 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26978 Z= 0.110 Angle : 0.567 9.559 36840 Z= 0.272 Chirality : 0.045 0.281 4316 Planarity : 0.003 0.039 4653 Dihedral : 6.601 59.226 4788 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.95 % Allowed : 11.06 % Favored : 87.98 % 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: -0.61 (0.14), residues: 3240 helix: 1.51 (0.21), residues: 687 sheet: -0.15 (0.18), residues: 747 loop : -1.31 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP C 254 HIS 0.003 0.001 HIS A1040 PHE 0.015 0.001 PHE B 29 TYR 0.017 0.001 TYR B1130 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 53) link_NAG-ASN : angle 2.30439 ( 159) link_BETA1-4 : bond 0.00509 ( 6) link_BETA1-4 : angle 3.49954 ( 18) hydrogen bonds : bond 0.03370 ( 969) hydrogen bonds : angle 5.06018 ( 2613) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.48836 ( 84) covalent geometry : bond 0.00251 (26877) covalent geometry : angle 0.53819 (36579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 2.677 Fit side-chains REVERT: A 249 MET cc_start: 0.6416 (mpp) cc_final: 0.4833 (ptp) REVERT: A 894 MET cc_start: 0.9094 (tpp) cc_final: 0.8543 (mmt) REVERT: B 249 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.3231 (ppp) REVERT: B 254 TRP cc_start: 0.7775 (p90) cc_final: 0.7471 (p90) REVERT: B 732 MET cc_start: 0.9221 (mmm) cc_final: 0.8822 (mtp) REVERT: B 1130 TYR cc_start: 0.8184 (t80) cc_final: 0.7904 (t80) REVERT: C 118 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8732 (tp) REVERT: C 249 MET cc_start: 0.7659 (pmm) cc_final: 0.7403 (pmm) REVERT: C 254 TRP cc_start: 0.7685 (p-90) cc_final: 0.7460 (p-90) outliers start: 27 outliers final: 23 residues processed: 83 average time/residue: 0.3255 time to fit residues: 48.4560 Evaluate side-chains 80 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 332 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1086 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 105 optimal weight: 0.0870 chunk 205 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 276 optimal weight: 0.3980 chunk 150 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061416 restraints weight = 56624.172| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.60 r_work: 0.2686 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26978 Z= 0.117 Angle : 0.567 9.624 36840 Z= 0.271 Chirality : 0.045 0.278 4316 Planarity : 0.003 0.038 4653 Dihedral : 6.556 59.458 4788 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.99 % Allowed : 11.10 % Favored : 87.91 % 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: -0.59 (0.15), residues: 3240 helix: 1.20 (0.21), residues: 726 sheet: -0.09 (0.19), residues: 744 loop : -1.23 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 254 HIS 0.004 0.001 HIS A1040 PHE 0.016 0.001 PHE B 29 TYR 0.016 0.001 TYR B1059 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 53) link_NAG-ASN : angle 2.28849 ( 159) link_BETA1-4 : bond 0.00463 ( 6) link_BETA1-4 : angle 3.46991 ( 18) hydrogen bonds : bond 0.03368 ( 969) hydrogen bonds : angle 5.02168 ( 2613) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.51313 ( 84) covalent geometry : bond 0.00270 (26877) covalent geometry : angle 0.53838 (36579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11538.59 seconds wall clock time: 203 minutes 20.80 seconds (12200.80 seconds total)