Starting phenix.real_space_refine on Sun Jul 5 08:25:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_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_34036/07_2026/7yqv_34036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqv_34036/07_2026/7yqv_34036.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 15 Time building chain proxies: 6.03, per 1000 atoms: 0.23 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.06 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: 5.48 Time building geometry restraints manager: 2.90 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 - 17.94: 14204 17.94 - 35.89: 1181 35.89 - 53.83: 183 53.83 - 71.77: 40 71.77 - 89.71: 28 Dihedral angle restraints: 15636 sinusoidal: 6045 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 15633 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: 2.120 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.620 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 13.666 89.713 9360 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 are 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/Z covalent geometry : bond 0.00394 / 0.19 (27104) covalent geometry : angle 0.64392 / 0.33 (36916) SS BOND : bond 0.00269 / 0.19 ( 38) SS BOND : angle 1.24069 / 0.73 ( 76) hydrogen bonds : bond 0.15939 / 10.35 ( 745) hydrogen bonds : angle 6.60502 / 4.58 ( 2070) link_BETA1-4 : bond 0.00632 / 0.43 ( 9) link_BETA1-4 : angle 3.23980 / 1.99 ( 27) link_NAG-ASN : bond 0.00519 / 0.42 ( 51) link_NAG-ASN : angle 3.56910 / 2.24 ( 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 : 0.757 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: 0.6898 (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: 0.7444 (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: 0.6139 (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: 0.1760 time to fit residues: 117.9686 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 : 1.087 ------------------------------------------------------------------------------- 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... A 644 GLN A1002 GLN A1005 GLN B 188 ASN B 487 ASN B 607 GLN B1005 GLN B1125 ASN ** 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 = 0.4355 r_free = 0.4355 target = 0.184328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146237 restraints weight = 42929.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144210 restraints weight = 63429.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141808 restraints weight = 52705.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140807 restraints weight = 39216.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141304 restraints weight = 35432.341| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27202 Z= 0.163 Angle : 0.691 19.144 37172 Z= 0.340 Chirality : 0.049 0.378 4359 Planarity : 0.004 0.067 4708 Dihedral : 4.612 36.174 3529 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.59 % Favored : 91.32 % Rotamer: Outliers : 1.16 % Allowed : 8.29 % Favored : 90.55 % 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 are not related in a simple way. whole: -1.79 (0.14), residues: 3273 helix: 1.14 (0.22), residues: 613 sheet: -0.54 (0.20), residues: 578 loop : -2.27 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 158 TYR 0.022 0.001 TYR A 266 PHE 0.021 0.002 PHE A 238 TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (27104) covalent geometry : angle 0.64943 / 0.33 (36916) SS BOND : bond 0.00532 / 0.32 ( 38) SS BOND : angle 1.78964 / 1.01 ( 76) hydrogen bonds : bond 0.05429 / 3.61 ( 745) hydrogen bonds : angle 5.41193 / 3.78 ( 2070) link_BETA1-4 : bond 0.00825 / 0.60 ( 9) link_BETA1-4 : angle 3.12523 / 2.00 ( 27) link_NAG-ASN : bond 0.00635 / 0.49 ( 51) link_NAG-ASN : angle 3.29354 / 2.06 ( 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 267 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8245 (t0) cc_final: 0.7777 (m-40) REVERT: B 121 ASN cc_start: 0.5222 (t0) cc_final: 0.4811 (t0) REVERT: B 189 LEU cc_start: 0.6695 (pt) cc_final: 0.6450 (tt) REVERT: B 428 ASP cc_start: 0.6688 (p0) cc_final: 0.6473 (p0) REVERT: B 779 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7503 (mt0) REVERT: C 960 ASN cc_start: 0.8523 (t0) cc_final: 0.7828 (m-40) outliers start: 33 outliers final: 23 residues processed: 258 average time/residue: 0.1633 time to fit residues: 68.7238 Evaluate side-chains 200 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 1.9990 chunk 188 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 281 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.185307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.147375 restraints weight = 43060.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147007 restraints weight = 62829.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.146333 restraints weight = 54094.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145000 restraints weight = 43493.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145546 restraints weight = 37670.471| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2240 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= 0.117 Angle : 0.648 19.179 37172 Z= 0.316 Chirality : 0.047 0.386 4359 Planarity : 0.004 0.051 4708 Dihedral : 4.475 37.465 3529 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.70 % Favored : 92.21 % Rotamer: Outliers : 1.79 % Allowed : 10.61 % Favored : 87.60 % 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 are not related in a simple way. whole: -1.59 (0.14), residues: 3273 helix: 1.35 (0.22), residues: 612 sheet: -0.33 (0.20), residues: 598 loop : -2.19 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.026 0.001 TYR C 453 PHE 0.020 0.001 PHE A 238 TRP 0.021 0.001 TRP B 104 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (27104) covalent geometry : angle 0.60599 / 0.31 (36916) SS BOND : bond 0.00475 / 0.24 ( 38) SS BOND : angle 1.84147 / 1.07 ( 76) hydrogen bonds : bond 0.04430 / 2.92 ( 745) hydrogen bonds : angle 5.07276 / 3.54 ( 2070) link_BETA1-4 : bond 0.00755 / 0.52 ( 9) link_BETA1-4 : angle 2.72921 / 1.79 ( 27) link_NAG-ASN : bond 0.00715 / 0.56 ( 51) link_NAG-ASN : angle 3.22329 / 2.00 ( 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 256 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8217 (t0) cc_final: 0.7745 (m-40) REVERT: A 1019 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7222 (ttp80) REVERT: B 189 LEU cc_start: 0.6411 (pt) cc_final: 0.6163 (tt) REVERT: B 584 ILE cc_start: 0.6638 (mm) cc_final: 0.6218 (pt) REVERT: B 779 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7474 (mt0) REVERT: B 904 TYR cc_start: 0.6764 (m-10) cc_final: 0.6550 (m-10) REVERT: C 117 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7197 (mt) REVERT: C 424 LYS cc_start: 0.8523 (tttp) cc_final: 0.8254 (tttm) REVERT: C 960 ASN cc_start: 0.8473 (t0) cc_final: 0.7771 (m-40) outliers start: 51 outliers final: 33 residues processed: 240 average time/residue: 0.1456 time to fit residues: 59.2381 Evaluate side-chains 211 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL 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 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 188 ASN 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 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 931 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR 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 302 THR 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: 0.8980 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 246 optimal weight: 0.0020 chunk 297 optimal weight: 0.0070 chunk 314 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 316 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 188 ASN B 245 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1005 GLN B1088 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.185836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147635 restraints weight = 42759.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142030 restraints weight = 67723.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135625 restraints weight = 46481.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135959 restraints weight = 50528.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136330 restraints weight = 41829.573| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2499 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= 0.108 Angle : 0.626 19.468 37172 Z= 0.303 Chirality : 0.046 0.385 4359 Planarity : 0.004 0.051 4708 Dihedral : 4.332 36.960 3529 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.18 % Rotamer: Outliers : 2.07 % Allowed : 12.22 % Favored : 85.70 % 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 are not related in a simple way. whole: -1.45 (0.14), residues: 3273 helix: 1.50 (0.22), residues: 608 sheet: -0.19 (0.21), residues: 589 loop : -2.10 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.024 0.001 TYR C 453 PHE 0.031 0.001 PHE B 135 TRP 0.024 0.001 TRP A 104 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (27104) covalent geometry : angle 0.58441 / 0.29 (36916) SS BOND : bond 0.00395 / 0.21 ( 38) SS BOND : angle 1.62340 / 0.96 ( 76) hydrogen bonds : bond 0.04016 / 2.66 ( 745) hydrogen bonds : angle 4.88309 / 3.40 ( 2070) link_BETA1-4 : bond 0.00709 / 0.48 ( 9) link_BETA1-4 : angle 2.48155 / 1.64 ( 27) link_NAG-ASN : bond 0.00695 / 0.54 ( 51) link_NAG-ASN : angle 3.20820 / 2.00 ( 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 253 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8239 (t0) cc_final: 0.7769 (m-40) REVERT: B 189 LEU cc_start: 0.7320 (pt) cc_final: 0.6583 (tt) REVERT: B 584 ILE cc_start: 0.6808 (mm) cc_final: 0.6264 (pt) REVERT: B 779 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7514 (mt0) REVERT: B 904 TYR cc_start: 0.6804 (m-10) cc_final: 0.6459 (m-10) REVERT: B 1050 MET cc_start: 0.7641 (mtp) cc_final: 0.7410 (mtm) REVERT: C 117 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7146 (mt) REVERT: C 191 GLU cc_start: 0.7586 (mp0) cc_final: 0.7182 (mp0) REVERT: C 235 ILE cc_start: 0.5717 (mm) cc_final: 0.5457 (mm) REVERT: C 406 GLU cc_start: 0.7787 (pt0) cc_final: 0.7402 (pt0) REVERT: C 424 LYS cc_start: 0.8613 (tttp) cc_final: 0.8331 (tttm) REVERT: C 960 ASN cc_start: 0.8489 (t0) cc_final: 0.7852 (m-40) outliers start: 59 outliers final: 44 residues processed: 232 average time/residue: 0.1596 time to fit residues: 62.0658 Evaluate side-chains 216 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL 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 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 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 188 ASN 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 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 739 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE 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 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 302 THR 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 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 1114 ILE 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: 10.0000 chunk 229 optimal weight: 20.0000 chunk 216 optimal weight: 0.0570 chunk 40 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 301 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.0370 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 239 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 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 = 0.4342 r_free = 0.4342 target = 0.183245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145016 restraints weight = 42525.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144229 restraints weight = 69866.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142090 restraints weight = 51167.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141313 restraints weight = 45388.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141445 restraints weight = 42586.137| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2816 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= 0.136 Angle : 0.637 19.485 37172 Z= 0.311 Chirality : 0.047 0.363 4359 Planarity : 0.004 0.051 4708 Dihedral : 4.317 36.495 3529 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.25 % Favored : 91.66 % Rotamer: Outliers : 2.18 % Allowed : 12.86 % Favored : 84.97 % 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 are not related in a simple way. whole: -1.48 (0.14), residues: 3273 helix: 1.36 (0.22), residues: 609 sheet: -0.19 (0.21), residues: 578 loop : -2.09 (0.12), residues: 2086 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 0.027 0.001 PHE A 238 TRP 0.018 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (27104) covalent geometry : angle 0.59518 / 0.30 (36916) SS BOND : bond 0.00486 / 0.25 ( 38) SS BOND : angle 1.85845 / 1.10 ( 76) hydrogen bonds : bond 0.04594 / 3.06 ( 745) hydrogen bonds : angle 4.88324 / 3.41 ( 2070) link_BETA1-4 : bond 0.00687 / 0.48 ( 9) link_BETA1-4 : angle 2.41830 / 1.61 ( 27) link_NAG-ASN : bond 0.00664 / 0.53 ( 51) link_NAG-ASN : angle 3.21101 / 2.00 ( 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 244 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6699 (ttt180) REVERT: A 960 ASN cc_start: 0.8281 (t0) cc_final: 0.7768 (m-40) REVERT: B 495 TYR cc_start: 0.7538 (m-10) cc_final: 0.7335 (m-10) REVERT: B 636 TYR cc_start: 0.5434 (m-10) cc_final: 0.5161 (m-10) REVERT: B 779 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7631 (mt0) REVERT: B 904 TYR cc_start: 0.6869 (m-10) cc_final: 0.6333 (m-10) REVERT: C 235 ILE cc_start: 0.6148 (mm) cc_final: 0.5814 (mm) REVERT: C 424 LYS cc_start: 0.8602 (tttp) cc_final: 0.8314 (tttm) REVERT: C 900 MET cc_start: 0.8296 (mtp) cc_final: 0.8004 (mtp) REVERT: C 906 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7847 (t80) REVERT: C 960 ASN cc_start: 0.8547 (t0) cc_final: 0.7856 (m-40) outliers start: 62 outliers final: 45 residues processed: 223 average time/residue: 0.1562 time to fit residues: 57.6240 Evaluate side-chains 212 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 319 ARG 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 943 SER 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 177 MET 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 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 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 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR 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 649 CYS 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 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE 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: 1.9990 chunk 184 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 324 optimal weight: 0.2980 chunk 240 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 268 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144795 restraints weight = 42433.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143894 restraints weight = 65502.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142988 restraints weight = 51040.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141723 restraints weight = 41647.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142432 restraints weight = 36611.523| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27202 Z= 0.108 Angle : 0.614 19.465 37172 Z= 0.297 Chirality : 0.046 0.367 4359 Planarity : 0.004 0.073 4708 Dihedral : 4.221 35.765 3529 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 2.35 % Allowed : 13.52 % Favored : 84.12 % 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 are not related in a simple way. whole: -1.38 (0.14), residues: 3273 helix: 1.43 (0.22), residues: 614 sheet: -0.05 (0.21), residues: 584 loop : -2.06 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.024 0.001 TYR C 453 PHE 0.021 0.001 PHE A 238 TRP 0.021 0.001 TRP A 104 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27104) covalent geometry : angle 0.57244 / 0.29 (36916) SS BOND : bond 0.00274 / 0.16 ( 38) SS BOND : angle 1.67415 / 0.99 ( 76) hydrogen bonds : bond 0.04131 / 2.75 ( 745) hydrogen bonds : angle 4.78344 / 3.35 ( 2070) link_BETA1-4 : bond 0.00677 / 0.47 ( 9) link_BETA1-4 : angle 2.29224 / 1.53 ( 27) link_NAG-ASN : bond 0.00667 / 0.53 ( 51) link_NAG-ASN : angle 3.18127 / 1.99 ( 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 243 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8259 (t0) cc_final: 0.7734 (m-40) REVERT: B 189 LEU cc_start: 0.6683 (pt) cc_final: 0.6181 (tt) REVERT: B 636 TYR cc_start: 0.5393 (m-10) cc_final: 0.5122 (m-10) REVERT: B 779 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7561 (mt0) REVERT: B 904 TYR cc_start: 0.6742 (m-10) cc_final: 0.6173 (m-10) REVERT: C 235 ILE cc_start: 0.6227 (mm) cc_final: 0.5861 (mm) REVERT: C 960 ASN cc_start: 0.8513 (t0) cc_final: 0.7803 (m-40) outliers start: 67 outliers final: 51 residues processed: 224 average time/residue: 0.1542 time to fit residues: 58.7898 Evaluate side-chains 212 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU 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 649 CYS 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 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 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 697 MET 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 866 THR 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 106 PHE 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 302 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 398 ASP 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 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER 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: 0.9980 chunk 139 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 114 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.184142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146123 restraints weight = 42576.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145012 restraints weight = 66056.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142298 restraints weight = 45800.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142100 restraints weight = 43727.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142271 restraints weight = 38498.362| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27202 Z= 0.108 Angle : 0.603 19.442 37172 Z= 0.291 Chirality : 0.046 0.361 4359 Planarity : 0.004 0.066 4708 Dihedral : 4.141 38.513 3529 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 2.04 % Allowed : 14.51 % Favored : 83.46 % 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 are not related in a simple way. whole: -1.33 (0.14), residues: 3273 helix: 1.52 (0.22), residues: 607 sheet: -0.03 (0.21), residues: 584 loop : -2.02 (0.13), residues: 2082 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 0.021 0.001 PHE C 133 TRP 0.017 0.001 TRP A 104 HIS 0.006 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (27104) covalent geometry : angle 0.56334 / 0.28 (36916) SS BOND : bond 0.00430 / 0.22 ( 38) SS BOND : angle 1.34126 / 0.77 ( 76) hydrogen bonds : bond 0.04023 / 2.67 ( 745) hydrogen bonds : angle 4.72573 / 3.30 ( 2070) link_BETA1-4 : bond 0.00638 / 0.44 ( 9) link_BETA1-4 : angle 2.19592 / 1.48 ( 27) link_NAG-ASN : bond 0.00655 / 0.52 ( 51) link_NAG-ASN : angle 3.15323 / 1.97 ( 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 229 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8274 (t0) cc_final: 0.7739 (m-40) REVERT: A 1019 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7396 (ttp80) REVERT: B 636 TYR cc_start: 0.5428 (m-10) cc_final: 0.5163 (m-10) REVERT: B 779 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7604 (mt0) REVERT: B 904 TYR cc_start: 0.6713 (m-10) cc_final: 0.6255 (m-10) REVERT: B 1050 MET cc_start: 0.7784 (mtp) cc_final: 0.7561 (mtm) REVERT: C 133 PHE cc_start: 0.6171 (m-80) cc_final: 0.5859 (m-80) REVERT: C 235 ILE cc_start: 0.6327 (mm) cc_final: 0.5923 (mm) REVERT: C 900 MET cc_start: 0.7808 (mtp) cc_final: 0.7498 (mtp) REVERT: C 906 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8254 (t80) REVERT: C 960 ASN cc_start: 0.8506 (t0) cc_final: 0.7797 (m-40) outliers start: 58 outliers final: 46 residues processed: 216 average time/residue: 0.1460 time to fit residues: 53.2745 Evaluate side-chains 209 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR 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 943 SER 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 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL 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 302 THR 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 711 SER 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 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: 0.0980 chunk 272 optimal weight: 5.9990 chunk 164 optimal weight: 0.0040 chunk 184 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 299 optimal weight: 0.0040 overall best weight: 0.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.185615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146599 restraints weight = 42705.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143789 restraints weight = 67622.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139206 restraints weight = 43865.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137782 restraints weight = 49474.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138596 restraints weight = 42022.886| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 27202 Z= 0.099 Angle : 0.603 19.399 37172 Z= 0.290 Chirality : 0.045 0.363 4359 Planarity : 0.004 0.062 4708 Dihedral : 4.076 37.123 3529 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.12 % Favored : 92.79 % Rotamer: Outliers : 1.90 % Allowed : 15.17 % Favored : 82.93 % 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 are not related in a simple way. whole: -1.26 (0.14), residues: 3273 helix: 1.60 (0.22), residues: 614 sheet: 0.00 (0.21), residues: 578 loop : -1.98 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.031 0.001 TYR B 495 PHE 0.019 0.001 PHE A 238 TRP 0.017 0.001 TRP B 104 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (27104) covalent geometry : angle 0.56270 / 0.28 (36916) SS BOND : bond 0.00264 / 0.15 ( 38) SS BOND : angle 1.78912 / 1.02 ( 76) hydrogen bonds : bond 0.03581 / 2.38 ( 745) hydrogen bonds : angle 4.64716 / 3.24 ( 2070) link_BETA1-4 : bond 0.00626 / 0.43 ( 9) link_BETA1-4 : angle 2.07077 / 1.40 ( 27) link_NAG-ASN : bond 0.00666 / 0.52 ( 51) link_NAG-ASN : angle 3.11164 / 1.95 ( 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 235 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6618 (tt) REVERT: A 104 TRP cc_start: 0.6041 (m-90) cc_final: 0.5804 (m-90) REVERT: A 960 ASN cc_start: 0.8247 (t0) cc_final: 0.7746 (m-40) REVERT: A 1019 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7482 (ttp80) REVERT: B 237 ARG cc_start: 0.6913 (tpt90) cc_final: 0.6696 (tpt90) REVERT: B 779 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7591 (mt0) REVERT: B 904 TYR cc_start: 0.6637 (m-10) cc_final: 0.6204 (m-10) REVERT: B 1005 GLN cc_start: 0.8165 (tt0) cc_final: 0.7936 (mt0) REVERT: C 235 ILE cc_start: 0.6429 (mm) cc_final: 0.6023 (mm) REVERT: C 900 MET cc_start: 0.8065 (mtp) cc_final: 0.7790 (mtp) REVERT: C 906 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8148 (t80) REVERT: C 960 ASN cc_start: 0.8457 (t0) cc_final: 0.7830 (m-40) REVERT: C 1050 MET cc_start: 0.8215 (ptp) cc_final: 0.7987 (ptm) outliers start: 54 outliers final: 44 residues processed: 221 average time/residue: 0.1471 time to fit residues: 54.2555 Evaluate side-chains 208 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 220 PHE Chi-restraints excluded: chain A residue 240 THR 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 534 VAL Chi-restraints excluded: chain A residue 620 VAL 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 697 MET Chi-restraints excluded: chain B residue 739 THR 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 106 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR 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 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 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: 2.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 295 optimal weight: 0.0970 chunk 314 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 304 optimal weight: 2.9990 chunk 162 optimal weight: 0.0980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 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 = 0.4346 r_free = 0.4346 target = 0.183652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.144275 restraints weight = 42344.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143258 restraints weight = 70048.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140432 restraints weight = 53365.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139590 restraints weight = 43682.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140265 restraints weight = 37044.300| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27202 Z= 0.122 Angle : 0.628 27.075 37172 Z= 0.299 Chirality : 0.046 0.350 4359 Planarity : 0.004 0.061 4708 Dihedral : 4.116 36.023 3529 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.51 % Rotamer: Outliers : 2.07 % Allowed : 15.49 % Favored : 82.44 % 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 are not related in a simple way. whole: -1.29 (0.14), residues: 3273 helix: 1.55 (0.22), residues: 613 sheet: 0.04 (0.21), residues: 573 loop : -2.01 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.026 0.001 TYR B 495 PHE 0.024 0.001 PHE A 238 TRP 0.017 0.001 TRP B 104 HIS 0.018 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27104) covalent geometry : angle 0.57923 / 0.29 (36916) SS BOND : bond 0.00401 / 0.21 ( 38) SS BOND : angle 1.25126 / 0.74 ( 76) hydrogen bonds : bond 0.04100 / 2.73 ( 745) hydrogen bonds : angle 4.66637 / 3.25 ( 2070) link_BETA1-4 : bond 0.00589 / 0.41 ( 9) link_BETA1-4 : angle 2.07940 / 1.40 ( 27) link_NAG-ASN : bond 0.00532 / 0.42 ( 51) link_NAG-ASN : angle 3.66446 / 2.57 ( 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 224 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7048 (tmt170) cc_final: 0.6094 (tmt170) REVERT: A 960 ASN cc_start: 0.8288 (t0) cc_final: 0.7773 (m-40) REVERT: A 1019 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7508 (ttp80) REVERT: B 904 TYR cc_start: 0.6799 (m-10) cc_final: 0.6289 (m-10) REVERT: C 235 ILE cc_start: 0.6767 (mm) cc_final: 0.6439 (mm) REVERT: C 900 MET cc_start: 0.8197 (mtp) cc_final: 0.7919 (mtp) REVERT: C 906 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8215 (t80) REVERT: C 960 ASN cc_start: 0.8540 (t0) cc_final: 0.7828 (m-40) outliers start: 59 outliers final: 46 residues processed: 210 average time/residue: 0.1540 time to fit residues: 55.2244 Evaluate side-chains 208 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL 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 332 ILE 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 697 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 762 GLN 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 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 390 LEU 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 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 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: 3.9990 chunk 216 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 225 optimal weight: 0.3980 chunk 64 optimal weight: 0.0870 chunk 189 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.184155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145208 restraints weight = 42270.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145763 restraints weight = 66399.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144153 restraints weight = 45877.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143502 restraints weight = 36905.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143808 restraints weight = 35258.360| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27202 Z= 0.107 Angle : 0.613 19.427 37172 Z= 0.295 Chirality : 0.046 0.355 4359 Planarity : 0.004 0.060 4708 Dihedral : 4.087 35.193 3529 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.48 % Rotamer: Outliers : 1.79 % Allowed : 15.77 % Favored : 82.44 % 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 are not related in a simple way. whole: -1.25 (0.14), residues: 3273 helix: 1.53 (0.22), residues: 619 sheet: 0.08 (0.21), residues: 580 loop : -1.99 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.026 0.001 TYR B 495 PHE 0.025 0.001 PHE C 133 TRP 0.020 0.001 TRP A 104 HIS 0.017 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (27104) covalent geometry : angle 0.56974 / 0.28 (36916) SS BOND : bond 0.00332 / 0.18 ( 38) SS BOND : angle 1.88713 / 1.10 ( 76) hydrogen bonds : bond 0.03909 / 2.60 ( 745) hydrogen bonds : angle 4.64189 / 3.24 ( 2070) link_BETA1-4 : bond 0.00603 / 0.41 ( 9) link_BETA1-4 : angle 2.06431 / 1.39 ( 27) link_NAG-ASN : bond 0.00546 / 0.42 ( 51) link_NAG-ASN : angle 3.21221 / 2.07 ( 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 217 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.022 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: 0.8270 (t0) cc_final: 0.7756 (m-40) REVERT: A 1019 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7512 (ttp80) REVERT: B 779 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7601 (mt0) REVERT: B 904 TYR cc_start: 0.6825 (m-10) cc_final: 0.6283 (m-10) REVERT: C 235 ILE cc_start: 0.6964 (mm) cc_final: 0.6654 (mm) REVERT: C 900 MET cc_start: 0.7871 (mtp) cc_final: 0.7624 (mtp) REVERT: C 906 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8204 (t80) REVERT: C 960 ASN cc_start: 0.8524 (t0) cc_final: 0.7802 (m-40) outliers start: 51 outliers final: 48 residues processed: 204 average time/residue: 0.1629 time to fit residues: 56.5402 Evaluate side-chains 210 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE 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 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 663 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 973 ILE 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 302 THR 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 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 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: 8.9990 chunk 61 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4339 r_free = 0.4339 target = 0.183074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144282 restraints weight = 42144.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143424 restraints weight = 65588.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140103 restraints weight = 45370.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139597 restraints weight = 43753.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139848 restraints weight = 40794.978| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3617 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= 0.122 Angle : 0.606 19.402 37172 Z= 0.293 Chirality : 0.046 0.355 4359 Planarity : 0.004 0.058 4708 Dihedral : 4.064 32.574 3529 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 1.69 % Allowed : 15.95 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3273 helix: 1.49 (0.22), residues: 613 sheet: 0.01 (0.21), residues: 581 loop : -2.01 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.025 0.001 TYR B 495 PHE 0.027 0.001 PHE A 238 TRP 0.016 0.001 TRP A 104 HIS 0.015 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (27104) covalent geometry : angle 0.56777 / 0.28 (36916) SS BOND : bond 0.00288 / 0.17 ( 38) SS BOND : angle 1.34313 / 0.79 ( 76) hydrogen bonds : bond 0.04244 / 2.83 ( 745) hydrogen bonds : angle 4.67571 / 3.26 ( 2070) link_BETA1-4 : bond 0.00603 / 0.42 ( 9) link_BETA1-4 : angle 2.10113 / 1.41 ( 27) link_NAG-ASN : bond 0.00536 / 0.42 ( 51) link_NAG-ASN : angle 3.11729 / 1.95 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4142.39 seconds wall clock time: 86 minutes 35.97 seconds (5195.97 seconds total)