Starting phenix.real_space_refine on Mon Aug 25 08:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqv_34036/08_2025/7yqv_34036.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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 111 5.16 5 C 16858 2.51 5 N 4331 2.21 5 O 5188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26488 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8540 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8536 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 5.39, per 1000 atoms: 0.20 Number of scatterers: 26488 At special positions: 0 Unit cell: (157.29, 160.5, 199.02, 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 111 16.00 O 5188 8.00 N 4331 7.00 C 16858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 74 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1302 " - " ASN B 74 " " NAG B1304 " - " ASN B 149 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 74 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1074 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1074 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 47 sheets defined 21.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.590A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.028A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.692A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.881A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 781 removed outlier: 4.164A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.717A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.409A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.725A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.683A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.571A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.647A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.583A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.977A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.594A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.037A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.652A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.083A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.975A pdb=" N PHE C 186 " --> pdb=" O GLN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.906A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.612A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.550A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.631A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.554A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.664A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.770A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.939A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.516A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.868A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.636A pdb=" N TRP A 64 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.675A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.670A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.583A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 4.060A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.566A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.738A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.006A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.694A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 removed outlier: 3.553A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.974A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.863A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.758A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.055A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.323A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.279A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.541A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.987A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.680A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.592A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.092A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.674A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.942A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 190 through 194 removed outlier: 3.716A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.561A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.672A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.298A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.420A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.830A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.553A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1089 through 1090 753 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.76 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: 8383 1.34 - 1.46: 6120 1.46 - 1.58: 12463 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 27104 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.12e+00 ... (remaining 27099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35796 1.71 - 3.42: 993 3.42 - 5.14: 103 5.14 - 6.85: 20 6.85 - 8.56: 4 Bond angle restraints: 36916 Sorted by residual: angle pdb=" C GLY C 232 " pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 121.97 130.53 -8.56 1.80e+00 3.09e-01 2.26e+01 angle pdb=" C ASP C 568 " pdb=" N ILE C 569 " pdb=" CA ILE C 569 " ideal model delta sigma weight residual 121.65 117.80 3.85 9.40e-01 1.13e+00 1.68e+01 angle pdb=" N ASP C 867 " pdb=" CA ASP C 867 " pdb=" C ASP C 867 " ideal model delta sigma weight residual 110.70 105.26 5.44 1.55e+00 4.16e-01 1.23e+01 angle pdb=" N GLU C 868 " pdb=" CA GLU C 868 " pdb=" C GLU C 868 " ideal model delta sigma weight residual 113.18 108.56 4.62 1.33e+00 5.65e-01 1.20e+01 angle pdb=" C ILE C 100 " pdb=" N ILE C 101 " pdb=" CA ILE C 101 " ideal model delta sigma weight residual 121.97 127.78 -5.81 1.80e+00 3.09e-01 1.04e+01 ... (remaining 36911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 15961 24.69 - 49.37: 820 49.37 - 74.06: 128 74.06 - 98.74: 43 98.74 - 123.43: 7 Dihedral angle restraints: 16959 sinusoidal: 7368 harmonic: 9591 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.19 -87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.23 70.77 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 147.90 -54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 16956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3961 0.086 - 0.172: 378 0.172 - 0.258: 10 0.258 - 0.344: 7 0.344 - 0.430: 3 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 4356 not shown) Planarity restraints: 4759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.003 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" CG ASN B 234 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 621 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO C 209 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.027 5.00e-02 4.00e+02 ... (remaining 4756 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 418 2.65 - 3.21: 24839 3.21 - 3.78: 37039 3.78 - 4.34: 49792 4.34 - 4.90: 82913 Nonbonded interactions: 195001 Sorted by model distance: nonbonded pdb=" O HIS C 69 " pdb=" OG SER C 247 " model vdw 2.090 3.040 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.158 3.120 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.169 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG C 214 " pdb=" OD1 ASP C 215 " model vdw 2.179 3.120 ... (remaining 194996 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' and (resid 25 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 346 or (resid 347 \ through 348 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 9 through 1315)) selection = (chain 'B' and (resid 25 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 194 or (resid 195 and (name N or n \ ame CA or name C or name O or name CB )) or resid 196 through 327 or (resid 328 \ through 329 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 0 through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 1315)) selection = (chain 'C' and (resid 25 through 189 or (resid 190 and (name N or name CA or nam \ e C or name O or name CB )) or resid 191 through 194 or (resid 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 327 or (resid 3 \ 28 through 329 and (name N or name CA or name C or name O or name CB )) or resid \ 330 through 1315)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.270 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.004 0.076 27202 Z= 0.187 Angle : 0.689 19.700 37172 Z= 0.339 Chirality : 0.049 0.430 4359 Planarity : 0.004 0.056 4708 Dihedral : 14.886 123.428 10683 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.14 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.14), residues: 3273 helix: 1.27 (0.23), residues: 599 sheet: -0.79 (0.19), residues: 611 loop : -2.27 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.026 0.001 TYR B 160 PHE 0.033 0.001 PHE A 192 TRP 0.020 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00394 (27104) covalent geometry : angle 0.64392 (36916) SS BOND : bond 0.00269 ( 38) SS BOND : angle 1.24069 ( 76) hydrogen bonds : bond 0.15939 ( 745) hydrogen bonds : angle 6.60502 ( 2070) link_BETA1-4 : bond 0.00632 ( 9) link_BETA1-4 : angle 3.23980 ( 27) link_NAG-ASN : bond 0.00519 ( 51) link_NAG-ASN : angle 3.56910 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5705 (m-90) cc_final: 0.5347 (m-90) REVERT: A 110 LEU cc_start: 0.5930 (tp) cc_final: 0.5723 (mp) REVERT: A 189 LEU cc_start: 0.7325 (tp) cc_final: 0.7102 (tp) REVERT: A 207 HIS cc_start: 0.7134 (t-90) cc_final: 0.6929 (t70) REVERT: A 554 GLU cc_start: 0.7470 (pp20) cc_final: 0.7259 (pt0) REVERT: A 725 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7629 (tt0) REVERT: A 868 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 900 MET cc_start: 0.7962 (mtp) cc_final: 0.7734 (mtt) REVERT: A 960 ASN cc_start: 0.7870 (t0) cc_final: 0.7396 (m-40) REVERT: A 1135 ASN cc_start: 0.8682 (t0) cc_final: 0.8379 (t0) REVERT: A 1138 TYR cc_start: 0.6897 (t80) cc_final: 0.6503 (t80) REVERT: B 54 LEU cc_start: 0.8528 (mp) cc_final: 0.8233 (tp) REVERT: B 189 LEU cc_start: 0.7790 (pt) cc_final: 0.6902 (tt) REVERT: B 779 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7511 (mt0) REVERT: B 823 PHE cc_start: 0.7740 (m-80) cc_final: 0.7445 (m-10) REVERT: B 969 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8513 (ttmm) REVERT: C 28 TYR cc_start: 0.6722 (m-10) cc_final: 0.6138 (m-10) REVERT: C 424 LYS cc_start: 0.8586 (tppt) cc_final: 0.8299 (ttmm) REVERT: C 461 LEU cc_start: 0.7806 (tp) cc_final: 0.7441 (tp) REVERT: C 462 LYS cc_start: 0.8245 (mtmm) cc_final: 0.8021 (mmtm) REVERT: C 960 ASN cc_start: 0.8116 (t0) cc_final: 0.7267 (m-40) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.1600 time to fit residues: 107.2361 Evaluate side-chains 203 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0030 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 245 HIS B 487 ASN B 607 GLN B 992 GLN B1005 GLN B1125 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.186292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.155600 restraints weight = 42520.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.152183 restraints weight = 67848.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149482 restraints weight = 58928.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149511 restraints weight = 56897.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149169 restraints weight = 40861.484| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27202 Z= 0.167 Angle : 0.712 19.296 37172 Z= 0.348 Chirality : 0.049 0.398 4359 Planarity : 0.005 0.065 4708 Dihedral : 9.742 102.104 4852 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 1.19 % Allowed : 8.75 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.14), residues: 3273 helix: 1.07 (0.22), residues: 613 sheet: -0.52 (0.20), residues: 571 loop : -2.27 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 454 TYR 0.024 0.002 TYR A 266 PHE 0.023 0.002 PHE A 238 TRP 0.015 0.001 TRP A 64 HIS 0.007 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00383 (27104) covalent geometry : angle 0.67081 (36916) SS BOND : bond 0.00357 ( 38) SS BOND : angle 1.55212 ( 76) hydrogen bonds : bond 0.05239 ( 745) hydrogen bonds : angle 5.37598 ( 2070) link_BETA1-4 : bond 0.00763 ( 9) link_BETA1-4 : angle 3.09862 ( 27) link_NAG-ASN : bond 0.00678 ( 51) link_NAG-ASN : angle 3.44418 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8252 (t0) cc_final: 0.7745 (m-40) REVERT: A 1019 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7421 (ttp80) REVERT: B 121 ASN cc_start: 0.4843 (t0) cc_final: 0.4446 (t0) REVERT: B 428 ASP cc_start: 0.6620 (p0) cc_final: 0.6417 (p0) REVERT: B 584 ILE cc_start: 0.6532 (mm) cc_final: 0.6123 (pt) REVERT: B 779 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7653 (mt0) REVERT: C 960 ASN cc_start: 0.8520 (t0) cc_final: 0.7832 (m-40) outliers start: 34 outliers final: 23 residues processed: 263 average time/residue: 0.1535 time to fit residues: 65.0166 Evaluate side-chains 197 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 289 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 219 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 chunk 281 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1002 GLN A1005 GLN B 188 ASN B 211 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146063 restraints weight = 42994.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144986 restraints weight = 61551.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145826 restraints weight = 54546.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144846 restraints weight = 40092.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145222 restraints weight = 39670.226| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27202 Z= 0.118 Angle : 0.651 19.149 37172 Z= 0.316 Chirality : 0.047 0.362 4359 Planarity : 0.004 0.050 4708 Dihedral : 8.660 97.670 4852 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 1.86 % Allowed : 11.20 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 3273 helix: 1.34 (0.22), residues: 612 sheet: -0.33 (0.21), residues: 579 loop : -2.18 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.025 0.001 TYR C 453 PHE 0.019 0.001 PHE C 133 TRP 0.020 0.001 TRP B 104 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00262 (27104) covalent geometry : angle 0.60675 (36916) SS BOND : bond 0.00390 ( 38) SS BOND : angle 1.89963 ( 76) hydrogen bonds : bond 0.04457 ( 745) hydrogen bonds : angle 5.07433 ( 2070) link_BETA1-4 : bond 0.00754 ( 9) link_BETA1-4 : angle 2.78518 ( 27) link_NAG-ASN : bond 0.00715 ( 51) link_NAG-ASN : angle 3.31749 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6395 (ttt180) REVERT: A 960 ASN cc_start: 0.8224 (t0) cc_final: 0.7752 (m-40) REVERT: A 1019 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7208 (ttp80) REVERT: B 584 ILE cc_start: 0.6654 (mm) cc_final: 0.6237 (pt) REVERT: B 779 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7540 (mt0) REVERT: B 904 TYR cc_start: 0.6858 (m-10) cc_final: 0.6643 (m-10) REVERT: C 117 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7201 (mt) REVERT: C 235 ILE cc_start: 0.5910 (mm) cc_final: 0.5658 (mm) REVERT: C 811 LYS cc_start: 0.6459 (mtpp) cc_final: 0.6182 (mtpp) REVERT: C 960 ASN cc_start: 0.8492 (t0) cc_final: 0.7765 (m-40) outliers start: 53 outliers final: 33 residues processed: 237 average time/residue: 0.1410 time to fit residues: 56.0671 Evaluate side-chains 209 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 71 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 246 optimal weight: 0.4980 chunk 297 optimal weight: 0.1980 chunk 314 optimal weight: 0.9990 chunk 98 optimal weight: 0.0270 chunk 252 optimal weight: 9.9990 chunk 316 optimal weight: 0.0370 chunk 65 optimal weight: 0.8980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.186378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148197 restraints weight = 42729.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144998 restraints weight = 67891.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140303 restraints weight = 51502.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139891 restraints weight = 55099.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140749 restraints weight = 45609.410| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27202 Z= 0.105 Angle : 0.633 19.386 37172 Z= 0.303 Chirality : 0.046 0.369 4359 Planarity : 0.004 0.051 4708 Dihedral : 7.814 94.179 4852 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 1.76 % Allowed : 12.93 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.14), residues: 3273 helix: 1.57 (0.22), residues: 608 sheet: -0.07 (0.21), residues: 577 loop : -2.12 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 646 TYR 0.025 0.001 TYR C 453 PHE 0.032 0.001 PHE B 135 TRP 0.026 0.001 TRP A 104 HIS 0.002 0.000 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00222 (27104) covalent geometry : angle 0.58836 (36916) SS BOND : bond 0.00299 ( 38) SS BOND : angle 1.59314 ( 76) hydrogen bonds : bond 0.03846 ( 745) hydrogen bonds : angle 4.80782 ( 2070) link_BETA1-4 : bond 0.00727 ( 9) link_BETA1-4 : angle 2.53679 ( 27) link_NAG-ASN : bond 0.00710 ( 51) link_NAG-ASN : angle 3.35929 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8237 (t0) cc_final: 0.7767 (m-40) REVERT: A 1019 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7249 (ttp80) REVERT: B 779 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7539 (mt0) REVERT: B 904 TYR cc_start: 0.6655 (m-10) cc_final: 0.6320 (m-10) REVERT: C 117 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7114 (mt) REVERT: C 191 GLU cc_start: 0.7537 (mp0) cc_final: 0.7198 (mp0) REVERT: C 235 ILE cc_start: 0.5900 (mm) cc_final: 0.5604 (mm) REVERT: C 390 LEU cc_start: 0.8536 (mt) cc_final: 0.8157 (mt) REVERT: C 392 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: C 406 GLU cc_start: 0.7650 (pt0) cc_final: 0.7356 (pt0) REVERT: C 960 ASN cc_start: 0.8443 (t0) cc_final: 0.7817 (m-40) REVERT: C 1050 MET cc_start: 0.8205 (ptp) cc_final: 0.7969 (ptp) outliers start: 50 outliers final: 35 residues processed: 229 average time/residue: 0.1408 time to fit residues: 54.2389 Evaluate side-chains 210 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 31 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 394 ASN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 519 HIS C 580 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.179090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138906 restraints weight = 42293.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135438 restraints weight = 65927.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128970 restraints weight = 46549.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129193 restraints weight = 50843.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129632 restraints weight = 42560.362| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27202 Z= 0.226 Angle : 0.716 19.439 37172 Z= 0.351 Chirality : 0.049 0.374 4359 Planarity : 0.004 0.064 4708 Dihedral : 7.623 91.414 4852 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.29 % Favored : 90.62 % Rotamer: Outliers : 2.39 % Allowed : 13.84 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.14), residues: 3273 helix: 0.87 (0.21), residues: 611 sheet: -0.43 (0.21), residues: 581 loop : -2.15 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.025 0.002 TYR C 453 PHE 0.019 0.002 PHE C 377 TRP 0.019 0.002 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00558 (27104) covalent geometry : angle 0.67493 (36916) SS BOND : bond 0.00484 ( 38) SS BOND : angle 1.92769 ( 76) hydrogen bonds : bond 0.06275 ( 745) hydrogen bonds : angle 5.18756 ( 2070) link_BETA1-4 : bond 0.00835 ( 9) link_BETA1-4 : angle 2.86694 ( 27) link_NAG-ASN : bond 0.00643 ( 51) link_NAG-ASN : angle 3.38693 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6547 (m-90) cc_final: 0.6306 (m-90) REVERT: A 960 ASN cc_start: 0.8409 (t0) cc_final: 0.7858 (m-40) REVERT: B 339 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7276 (t70) REVERT: B 495 TYR cc_start: 0.7672 (m-10) cc_final: 0.7431 (m-10) REVERT: B 636 TYR cc_start: 0.5864 (m-10) cc_final: 0.5568 (m-10) REVERT: B 904 TYR cc_start: 0.6991 (m-10) cc_final: 0.6390 (m-10) REVERT: C 235 ILE cc_start: 0.6665 (mm) cc_final: 0.6276 (mm) REVERT: C 392 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: C 406 GLU cc_start: 0.7831 (pt0) cc_final: 0.7511 (pt0) REVERT: C 906 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 960 ASN cc_start: 0.8610 (t0) cc_final: 0.7994 (m-40) outliers start: 68 outliers final: 44 residues processed: 237 average time/residue: 0.1372 time to fit residues: 55.0441 Evaluate side-chains 213 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 192 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 324 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 268 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN A1002 GLN B 978 ASN B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.184479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142688 restraints weight = 41951.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142664 restraints weight = 51569.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138609 restraints weight = 38059.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137705 restraints weight = 37558.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138361 restraints weight = 35626.915| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27202 Z= 0.117 Angle : 0.699 35.027 37172 Z= 0.324 Chirality : 0.047 0.371 4359 Planarity : 0.004 0.058 4708 Dihedral : 7.412 89.887 4852 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.58 % Favored : 92.33 % Rotamer: Outliers : 2.28 % Allowed : 14.72 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3273 helix: 1.21 (0.22), residues: 620 sheet: -0.23 (0.21), residues: 580 loop : -2.13 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.025 0.001 TYR C 453 PHE 0.018 0.001 PHE C 374 TRP 0.018 0.001 TRP B 104 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00258 (27104) covalent geometry : angle 0.60783 (36916) SS BOND : bond 0.00313 ( 38) SS BOND : angle 1.90623 ( 76) hydrogen bonds : bond 0.04637 ( 745) hydrogen bonds : angle 4.90198 ( 2070) link_BETA1-4 : bond 0.00737 ( 9) link_BETA1-4 : angle 2.60846 ( 27) link_NAG-ASN : bond 0.00596 ( 51) link_NAG-ASN : angle 5.15126 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 176 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6644 (tt) REVERT: A 104 TRP cc_start: 0.6276 (m-90) cc_final: 0.6057 (m-90) REVERT: A 960 ASN cc_start: 0.8337 (t0) cc_final: 0.7779 (m-40) REVERT: B 636 TYR cc_start: 0.5616 (m-10) cc_final: 0.5370 (m-10) REVERT: B 904 TYR cc_start: 0.6928 (m-10) cc_final: 0.6448 (m-10) REVERT: C 235 ILE cc_start: 0.6586 (mm) cc_final: 0.6201 (mm) REVERT: C 266 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: C 906 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8088 (t80) REVERT: C 960 ASN cc_start: 0.8592 (t0) cc_final: 0.7868 (m-40) outliers start: 65 outliers final: 46 residues processed: 225 average time/residue: 0.1337 time to fit residues: 51.6179 Evaluate side-chains 211 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 3.9990 chunk 139 optimal weight: 0.0980 chunk 326 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 148 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.184382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144529 restraints weight = 42099.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138916 restraints weight = 57086.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134238 restraints weight = 42452.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134614 restraints weight = 37619.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134820 restraints weight = 36638.775| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27202 Z= 0.125 Angle : 0.661 28.271 37172 Z= 0.312 Chirality : 0.047 0.363 4359 Planarity : 0.004 0.055 4708 Dihedral : 7.378 86.920 4852 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.07 % Favored : 91.84 % Rotamer: Outliers : 2.21 % Allowed : 15.45 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.14), residues: 3273 helix: 1.29 (0.22), residues: 614 sheet: -0.15 (0.21), residues: 571 loop : -2.05 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.024 0.001 TYR C 453 PHE 0.022 0.001 PHE C 133 TRP 0.019 0.001 TRP B 104 HIS 0.018 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00287 (27104) covalent geometry : angle 0.60171 (36916) SS BOND : bond 0.00345 ( 38) SS BOND : angle 1.82951 ( 76) hydrogen bonds : bond 0.04492 ( 745) hydrogen bonds : angle 4.81175 ( 2070) link_BETA1-4 : bond 0.00643 ( 9) link_BETA1-4 : angle 2.44496 ( 27) link_NAG-ASN : bond 0.00628 ( 51) link_NAG-ASN : angle 3.99966 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7827 (tmt170) cc_final: 0.7482 (tmt170) REVERT: A 319 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6647 (ttt180) REVERT: A 960 ASN cc_start: 0.8359 (t0) cc_final: 0.8097 (t0) REVERT: B 636 TYR cc_start: 0.5905 (m-10) cc_final: 0.5656 (m-10) REVERT: B 904 TYR cc_start: 0.6993 (m-10) cc_final: 0.6454 (m-10) REVERT: C 235 ILE cc_start: 0.7018 (mm) cc_final: 0.6611 (mm) REVERT: C 266 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: C 906 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8176 (t80) REVERT: C 960 ASN cc_start: 0.8572 (t0) cc_final: 0.7855 (m-40) outliers start: 63 outliers final: 40 residues processed: 218 average time/residue: 0.1576 time to fit residues: 58.0795 Evaluate side-chains 205 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 129 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 184 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 66 HIS ** 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 = 0.4166 r_free = 0.4166 target = 0.172285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131941 restraints weight = 41232.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128277 restraints weight = 68601.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125351 restraints weight = 54981.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125473 restraints weight = 51103.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125445 restraints weight = 41243.965| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27202 Z= 0.202 Angle : 0.689 19.037 37172 Z= 0.336 Chirality : 0.048 0.381 4359 Planarity : 0.004 0.066 4708 Dihedral : 7.666 106.940 4852 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 2.35 % Allowed : 15.53 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.14), residues: 3273 helix: 1.00 (0.21), residues: 609 sheet: -0.36 (0.21), residues: 558 loop : -2.11 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.023 0.002 TYR B 265 PHE 0.019 0.002 PHE C 374 TRP 0.021 0.002 TRP A 104 HIS 0.014 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00503 (27104) covalent geometry : angle 0.65020 (36916) SS BOND : bond 0.00582 ( 38) SS BOND : angle 1.63484 ( 76) hydrogen bonds : bond 0.05780 ( 745) hydrogen bonds : angle 5.02005 ( 2070) link_BETA1-4 : bond 0.00673 ( 9) link_BETA1-4 : angle 2.59312 ( 27) link_NAG-ASN : bond 0.00507 ( 51) link_NAG-ASN : angle 3.29467 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6646 (ttt180) REVERT: A 759 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 960 ASN cc_start: 0.8436 (t0) cc_final: 0.8175 (t0) REVERT: A 1005 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: A 1017 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 339 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.7086 (t70) REVERT: B 636 TYR cc_start: 0.5623 (m-10) cc_final: 0.5339 (m-10) REVERT: B 759 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 904 TYR cc_start: 0.7027 (m-10) cc_final: 0.6432 (m-10) REVERT: C 235 ILE cc_start: 0.7350 (mm) cc_final: 0.7046 (mm) REVERT: C 241 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5942 (pp) REVERT: C 266 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: C 906 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 960 ASN cc_start: 0.8596 (t0) cc_final: 0.7969 (m-40) outliers start: 67 outliers final: 47 residues processed: 223 average time/residue: 0.1531 time to fit residues: 57.8859 Evaluate side-chains 217 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 295 optimal weight: 0.3980 chunk 314 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** 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 = 0.4196 r_free = 0.4196 target = 0.175071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141125 restraints weight = 41105.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137348 restraints weight = 68499.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133582 restraints weight = 65465.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132915 restraints weight = 64963.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131809 restraints weight = 50379.916| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27202 Z= 0.113 Angle : 0.641 19.019 37172 Z= 0.309 Chirality : 0.046 0.388 4359 Planarity : 0.004 0.065 4708 Dihedral : 7.457 109.229 4852 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 1.86 % Allowed : 16.30 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.14), residues: 3273 helix: 1.30 (0.22), residues: 614 sheet: -0.24 (0.21), residues: 574 loop : -2.07 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.028 0.001 TYR B 170 PHE 0.020 0.001 PHE B 133 TRP 0.022 0.001 TRP A 104 HIS 0.013 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00254 (27104) covalent geometry : angle 0.59696 (36916) SS BOND : bond 0.00285 ( 38) SS BOND : angle 2.05268 ( 76) hydrogen bonds : bond 0.04524 ( 745) hydrogen bonds : angle 4.82817 ( 2070) link_BETA1-4 : bond 0.00665 ( 9) link_BETA1-4 : angle 2.44870 ( 27) link_NAG-ASN : bond 0.00547 ( 51) link_NAG-ASN : angle 3.25017 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7595 (tmt170) cc_final: 0.7331 (ttt-90) REVERT: A 319 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6554 (ttt180) REVERT: A 759 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6473 (t80) REVERT: A 960 ASN cc_start: 0.8384 (t0) cc_final: 0.8109 (t0) REVERT: B 636 TYR cc_start: 0.5569 (m-10) cc_final: 0.5239 (m-10) REVERT: B 759 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 779 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7713 (mt0) REVERT: B 900 MET cc_start: 0.7608 (mtp) cc_final: 0.7302 (mtp) REVERT: B 904 TYR cc_start: 0.6861 (m-10) cc_final: 0.6313 (m-10) REVERT: C 235 ILE cc_start: 0.7168 (mm) cc_final: 0.6960 (mm) REVERT: C 266 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: C 906 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8164 (t80) REVERT: C 960 ASN cc_start: 0.8499 (t0) cc_final: 0.7828 (m-40) outliers start: 53 outliers final: 40 residues processed: 211 average time/residue: 0.1498 time to fit residues: 53.3142 Evaluate side-chains 208 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 149 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 122 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** 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 = 0.4182 r_free = 0.4182 target = 0.173795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139679 restraints weight = 41071.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135711 restraints weight = 70336.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133028 restraints weight = 62397.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132643 restraints weight = 63070.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131791 restraints weight = 49144.984| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27202 Z= 0.142 Angle : 0.646 18.845 37172 Z= 0.313 Chirality : 0.047 0.390 4359 Planarity : 0.004 0.063 4708 Dihedral : 7.404 111.746 4852 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % Rotamer: Outliers : 1.72 % Allowed : 16.61 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.14), residues: 3273 helix: 1.26 (0.22), residues: 614 sheet: -0.19 (0.21), residues: 562 loop : -2.06 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.022 0.001 TYR C 453 PHE 0.018 0.001 PHE C 392 TRP 0.019 0.001 TRP B 64 HIS 0.012 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00343 (27104) covalent geometry : angle 0.60408 (36916) SS BOND : bond 0.00385 ( 38) SS BOND : angle 2.01878 ( 76) hydrogen bonds : bond 0.04839 ( 745) hydrogen bonds : angle 4.84564 ( 2070) link_BETA1-4 : bond 0.00629 ( 9) link_BETA1-4 : angle 2.40764 ( 27) link_NAG-ASN : bond 0.00520 ( 51) link_NAG-ASN : angle 3.21424 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6561 (ttt180) REVERT: A 759 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.6649 (t80) REVERT: A 960 ASN cc_start: 0.8399 (t0) cc_final: 0.8140 (t0) REVERT: A 1005 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8093 (tp40) REVERT: B 636 TYR cc_start: 0.5596 (m-10) cc_final: 0.5212 (m-10) REVERT: B 759 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 900 MET cc_start: 0.7681 (mtp) cc_final: 0.7440 (mtp) REVERT: B 904 TYR cc_start: 0.6972 (m-10) cc_final: 0.6384 (m-10) REVERT: C 906 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7935 (t80) REVERT: C 960 ASN cc_start: 0.8553 (t0) cc_final: 0.7905 (m-40) REVERT: C 981 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8357 (tt) outliers start: 49 outliers final: 41 residues processed: 207 average time/residue: 0.1447 time to fit residues: 51.1409 Evaluate side-chains 201 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 115 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 264 optimal weight: 0.0010 chunk 198 optimal weight: 0.0030 chunk 103 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.173813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140903 restraints weight = 41032.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137956 restraints weight = 63860.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135775 restraints weight = 48222.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133830 restraints weight = 55124.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132520 restraints weight = 51858.426| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 27202 Z= 0.169 Angle : 0.802 59.165 37172 Z= 0.416 Chirality : 0.049 0.782 4359 Planarity : 0.004 0.062 4708 Dihedral : 7.402 111.740 4852 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.19 % Favored : 91.72 % Rotamer: Outliers : 1.79 % Allowed : 16.61 % Favored : 81.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.14), residues: 3273 helix: 1.25 (0.22), residues: 614 sheet: -0.20 (0.21), residues: 562 loop : -2.06 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.021 0.001 TYR C 453 PHE 0.015 0.001 PHE C 392 TRP 0.021 0.002 TRP C 64 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00384 (27104) covalent geometry : angle 0.76533 (36916) SS BOND : bond 0.01106 ( 38) SS BOND : angle 2.69968 ( 76) hydrogen bonds : bond 0.04798 ( 745) hydrogen bonds : angle 4.84923 ( 2070) link_BETA1-4 : bond 0.00594 ( 9) link_BETA1-4 : angle 2.40339 ( 27) link_NAG-ASN : bond 0.00516 ( 51) link_NAG-ASN : angle 3.21277 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3909.19 seconds wall clock time: 68 minutes 37.62 seconds (4117.62 seconds total)