Starting phenix.real_space_refine on Mon Jun 23 02:36:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqv_34036/06_2025/7yqv_34036.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP: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: {'TYR:plan': 1, 'ARG:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 16.43, per 1000 atoms: 0.62 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: 7.05 Conformation dependent library (CDL) restraints added in 3.7 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: 3.35 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: 10.76 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8383 1.34 - 1.46: 6120 1.46 - 1.58: 12463 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 27104 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.12e+00 ... (remaining 27099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35796 1.71 - 3.42: 993 3.42 - 5.14: 103 5.14 - 6.85: 20 6.85 - 8.56: 4 Bond angle restraints: 36916 Sorted by residual: angle pdb=" C GLY C 232 " pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 121.97 130.53 -8.56 1.80e+00 3.09e-01 2.26e+01 angle pdb=" C ASP C 568 " pdb=" N ILE C 569 " pdb=" CA ILE C 569 " ideal model delta sigma weight residual 121.65 117.80 3.85 9.40e-01 1.13e+00 1.68e+01 angle pdb=" N ASP C 867 " pdb=" CA ASP C 867 " pdb=" C ASP C 867 " ideal model delta sigma weight residual 110.70 105.26 5.44 1.55e+00 4.16e-01 1.23e+01 angle pdb=" N GLU C 868 " pdb=" CA GLU C 868 " pdb=" C GLU C 868 " ideal model delta sigma weight residual 113.18 108.56 4.62 1.33e+00 5.65e-01 1.20e+01 angle pdb=" C ILE C 100 " pdb=" N ILE C 101 " pdb=" CA ILE C 101 " ideal model delta sigma weight residual 121.97 127.78 -5.81 1.80e+00 3.09e-01 1.04e+01 ... (remaining 36911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 15961 24.69 - 49.37: 820 49.37 - 74.06: 128 74.06 - 98.74: 43 98.74 - 123.43: 7 Dihedral angle restraints: 16959 sinusoidal: 7368 harmonic: 9591 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.19 -87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.23 70.77 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 147.90 -54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 16956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3961 0.086 - 0.172: 378 0.172 - 0.258: 10 0.258 - 0.344: 7 0.344 - 0.430: 3 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 4356 not shown) Planarity restraints: 4759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.003 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" CG ASN B 234 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 621 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO C 209 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.027 5.00e-02 4.00e+02 ... (remaining 4756 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 418 2.65 - 3.21: 24839 3.21 - 3.78: 37039 3.78 - 4.34: 49792 4.34 - 4.90: 82913 Nonbonded interactions: 195001 Sorted by model distance: nonbonded pdb=" O HIS C 69 " pdb=" OG SER C 247 " model vdw 2.090 3.040 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.158 3.120 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.169 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG C 214 " pdb=" OD1 ASP C 215 " model vdw 2.179 3.120 ... (remaining 194996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 346 or (resid 347 \ through 348 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 9 through 1144 or resid 1301 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 1144 or resid 1301 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 1144 or resid 1301 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: 1.760 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: 1.200 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 63.080 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27202 Z= 0.187 Angle : 0.689 19.700 37172 Z= 0.339 Chirality : 0.049 0.430 4359 Planarity : 0.004 0.056 4708 Dihedral : 14.886 123.428 10683 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (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 TRP 0.020 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 PHE 0.033 0.001 PHE A 192 TYR 0.026 0.001 TYR B 160 ARG 0.008 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 51) link_NAG-ASN : angle 3.56910 ( 153) link_BETA1-4 : bond 0.00632 ( 9) link_BETA1-4 : angle 3.23980 ( 27) hydrogen bonds : bond 0.15939 ( 745) hydrogen bonds : angle 6.60502 ( 2070) SS BOND : bond 0.00269 ( 38) SS BOND : angle 1.24069 ( 76) covalent geometry : bond 0.00394 (27104) covalent geometry : angle 0.64392 (36916) *********************** 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 : 2.846 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: 0.5365 (m-90) REVERT: A 110 LEU cc_start: 0.5930 (tp) cc_final: 0.5725 (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: 0.6928 (t70) REVERT: A 554 GLU cc_start: 0.7470 (pp20) cc_final: 0.7258 (pt0) REVERT: A 725 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7632 (tt0) REVERT: A 868 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 900 MET cc_start: 0.7962 (mtp) cc_final: 0.7733 (mtt) REVERT: A 960 ASN cc_start: 0.7870 (t0) cc_final: 0.7397 (m-40) REVERT: A 1135 ASN cc_start: 0.8682 (t0) cc_final: 0.8379 (t0) REVERT: A 1138 TYR cc_start: 0.6897 (t80) cc_final: 0.6503 (t80) REVERT: B 54 LEU cc_start: 0.8528 (mp) cc_final: 0.8231 (tp) REVERT: B 189 LEU cc_start: 0.7790 (pt) cc_final: 0.6901 (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: 0.8514 (ttmm) REVERT: C 424 LYS cc_start: 0.8586 (tppt) cc_final: 0.8301 (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: 0.3992 time to fit residues: 264.7406 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 : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.0030 chunk 190 optimal weight: 0.6980 chunk 296 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 487 ASN B 607 GLN B1005 GLN B1125 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.189973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152514 restraints weight = 43578.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149357 restraints weight = 58930.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142739 restraints weight = 35585.079| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27202 Z= 0.128 Angle : 0.674 19.186 37172 Z= 0.329 Chirality : 0.048 0.391 4359 Planarity : 0.004 0.067 4708 Dihedral : 10.048 111.154 4852 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.37 % Favored : 91.54 % Rotamer: Outliers : 1.16 % Allowed : 7.80 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3273 helix: 1.36 (0.22), residues: 613 sheet: -0.46 (0.20), residues: 578 loop : -2.22 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS C1101 PHE 0.020 0.001 PHE C 65 TYR 0.021 0.001 TYR B 265 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 51) link_NAG-ASN : angle 3.33977 ( 153) link_BETA1-4 : bond 0.00837 ( 9) link_BETA1-4 : angle 3.06706 ( 27) hydrogen bonds : bond 0.04868 ( 745) hydrogen bonds : angle 5.35924 ( 2070) SS BOND : bond 0.00445 ( 38) SS BOND : angle 1.62568 ( 76) covalent geometry : bond 0.00281 (27104) covalent geometry : angle 0.63138 (36916) *********************** 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 281 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 3.006 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 237 ARG cc_start: 0.6725 (ptp-110) cc_final: 0.6480 (ptt90) REVERT: A 238 PHE cc_start: 0.6934 (t80) cc_final: 0.6616 (t80) REVERT: A 960 ASN cc_start: 0.8238 (t0) cc_final: 0.7787 (m-40) REVERT: A 1019 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7541 (ttp80) REVERT: B 121 ASN cc_start: 0.5859 (t0) cc_final: 0.5419 (t0) REVERT: B 189 LEU cc_start: 0.7183 (pt) cc_final: 0.6805 (tt) REVERT: B 779 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7635 (mt0) REVERT: C 850 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 960 ASN cc_start: 0.8508 (t0) cc_final: 0.7801 (m-40) outliers start: 33 outliers final: 25 residues processed: 270 average time/residue: 0.3847 time to fit residues: 167.6649 Evaluate side-chains 206 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 274 THR 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 551 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER 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 772 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 850 ILE 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 228 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B 188 ASN B 211 ASN B 245 HIS B 394 ASN B 992 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.182959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142815 restraints weight = 42478.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138732 restraints weight = 57838.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140058 restraints weight = 53412.374| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27202 Z= 0.164 Angle : 0.688 19.024 37172 Z= 0.336 Chirality : 0.048 0.381 4359 Planarity : 0.004 0.049 4708 Dihedral : 8.707 97.482 4852 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.37 % Favored : 91.51 % Rotamer: Outliers : 1.83 % Allowed : 11.03 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3273 helix: 1.14 (0.22), residues: 613 sheet: -0.46 (0.20), residues: 587 loop : -2.19 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 104 HIS 0.004 0.001 HIS A1048 PHE 0.020 0.002 PHE C 133 TYR 0.027 0.001 TYR C 453 ARG 0.005 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 51) link_NAG-ASN : angle 3.33400 ( 153) link_BETA1-4 : bond 0.00774 ( 9) link_BETA1-4 : angle 2.87860 ( 27) hydrogen bonds : bond 0.05232 ( 745) hydrogen bonds : angle 5.16601 ( 2070) SS BOND : bond 0.00702 ( 38) SS BOND : angle 2.18991 ( 76) covalent geometry : bond 0.00390 (27104) covalent geometry : angle 0.64414 (36916) *********************** 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 258 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 2.936 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: 0.8265 (t0) cc_final: 0.7800 (m-40) REVERT: A 1019 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7434 (ttp80) REVERT: B 189 LEU cc_start: 0.6688 (pt) cc_final: 0.6296 (tt) REVERT: B 584 ILE cc_start: 0.6691 (mm) cc_final: 0.6196 (pt) REVERT: B 779 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7730 (mt0) REVERT: B 904 TYR cc_start: 0.6985 (m-10) cc_final: 0.6700 (m-10) REVERT: C 424 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8173 (tttm) REVERT: C 900 MET cc_start: 0.8278 (mtp) cc_final: 0.8019 (mtp) REVERT: C 960 ASN cc_start: 0.8564 (t0) cc_final: 0.7882 (m-40) outliers start: 52 outliers final: 37 residues processed: 241 average time/residue: 0.3451 time to fit residues: 138.7116 Evaluate side-chains 216 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 3.090 ------------------------------------------------------------------------------- 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 281 GLU 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 228 ASP 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 551 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE 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 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 525 CYS 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 813 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 220 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 11 optimal weight: 0.0170 chunk 117 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 196 ASN B 978 ASN B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN 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 = 0.183995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142594 restraints weight = 42796.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138767 restraints weight = 55189.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140034 restraints weight = 48594.616| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27202 Z= 0.118 Angle : 0.635 19.449 37172 Z= 0.307 Chirality : 0.047 0.384 4359 Planarity : 0.004 0.050 4708 Dihedral : 7.852 94.125 4852 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 1.86 % Allowed : 12.57 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3273 helix: 1.41 (0.22), residues: 603 sheet: -0.16 (0.21), residues: 564 loop : -2.13 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 104 HIS 0.002 0.000 HIS A 339 PHE 0.027 0.001 PHE B 135 TYR 0.024 0.001 TYR C 453 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 51) link_NAG-ASN : angle 3.39360 ( 153) link_BETA1-4 : bond 0.00745 ( 9) link_BETA1-4 : angle 2.63851 ( 27) hydrogen bonds : bond 0.04319 ( 745) hydrogen bonds : angle 4.89582 ( 2070) SS BOND : bond 0.00346 ( 38) SS BOND : angle 1.77708 ( 76) covalent geometry : bond 0.00266 (27104) covalent geometry : angle 0.58842 (36916) *********************** 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 246 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8262 (t0) cc_final: 0.7771 (m-40) REVERT: A 1019 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7127 (ttp80) REVERT: B 189 LEU cc_start: 0.6857 (pt) cc_final: 0.6408 (tt) REVERT: B 636 TYR cc_start: 0.5396 (m-10) cc_final: 0.5157 (m-10) REVERT: B 779 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7754 (mt0) REVERT: B 904 TYR cc_start: 0.6885 (m-10) cc_final: 0.6447 (m-10) REVERT: C 117 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7185 (mt) REVERT: C 424 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8211 (tttm) REVERT: C 900 MET cc_start: 0.8166 (mtp) cc_final: 0.7838 (mtp) REVERT: C 960 ASN cc_start: 0.8459 (t0) cc_final: 0.7751 (m-40) outliers start: 53 outliers final: 35 residues processed: 227 average time/residue: 0.3325 time to fit residues: 125.4172 Evaluate side-chains 208 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 281 GLU 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 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 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE 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 977 LEU 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 398 ASP 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 813 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 42 optimal weight: 9.9990 chunk 263 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 305 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A1002 GLN B1005 GLN B1088 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.182023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139123 restraints weight = 41906.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137638 restraints weight = 55644.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138771 restraints weight = 47449.373| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27202 Z= 0.185 Angle : 0.684 19.415 37172 Z= 0.335 Chirality : 0.048 0.373 4359 Planarity : 0.004 0.049 4708 Dihedral : 7.551 90.991 4852 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 2.77 % Allowed : 13.07 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3273 helix: 0.93 (0.21), residues: 616 sheet: -0.33 (0.21), residues: 564 loop : -2.14 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 104 HIS 0.004 0.001 HIS C 49 PHE 0.018 0.002 PHE A 238 TYR 0.023 0.002 TYR C 453 ARG 0.005 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 51) link_NAG-ASN : angle 3.38043 ( 153) link_BETA1-4 : bond 0.00738 ( 9) link_BETA1-4 : angle 2.75605 ( 27) hydrogen bonds : bond 0.05785 ( 745) hydrogen bonds : angle 5.07801 ( 2070) SS BOND : bond 0.00402 ( 38) SS BOND : angle 1.91590 ( 76) covalent geometry : bond 0.00451 (27104) covalent geometry : angle 0.64111 (36916) *********************** 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 262 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 183 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6736 (ttt180) REVERT: A 960 ASN cc_start: 0.8398 (t0) cc_final: 0.8146 (t0) REVERT: B 189 LEU cc_start: 0.6923 (pt) cc_final: 0.6442 (tt) REVERT: B 339 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.7065 (t70) REVERT: B 636 TYR cc_start: 0.5719 (m-10) cc_final: 0.5414 (m-10) REVERT: B 904 TYR cc_start: 0.6903 (m-10) cc_final: 0.6359 (m-10) REVERT: C 424 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8250 (tttm) REVERT: C 906 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 960 ASN cc_start: 0.8594 (t0) cc_final: 0.7898 (m-40) outliers start: 79 outliers final: 49 residues processed: 240 average time/residue: 0.3210 time to fit residues: 130.1208 Evaluate side-chains 217 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 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 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 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 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 128 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 162 optimal weight: 0.1980 chunk 285 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1005 GLN B 978 ASN B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.184054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144074 restraints weight = 41921.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140579 restraints weight = 57283.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141889 restraints weight = 51664.001| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27202 Z= 0.120 Angle : 0.628 19.383 37172 Z= 0.304 Chirality : 0.047 0.522 4359 Planarity : 0.004 0.049 4708 Dihedral : 7.222 89.031 4852 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.58 % Favored : 92.33 % Rotamer: Outliers : 2.63 % Allowed : 14.61 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3273 helix: 1.23 (0.22), residues: 614 sheet: -0.24 (0.21), residues: 584 loop : -2.11 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.020 0.001 HIS B 49 PHE 0.017 0.001 PHE C 374 TYR 0.024 0.001 TYR C 453 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 51) link_NAG-ASN : angle 3.33545 ( 153) link_BETA1-4 : bond 0.00726 ( 9) link_BETA1-4 : angle 2.56922 ( 27) hydrogen bonds : bond 0.04590 ( 745) hydrogen bonds : angle 4.88609 ( 2070) SS BOND : bond 0.00358 ( 38) SS BOND : angle 1.60081 ( 76) covalent geometry : bond 0.00275 (27104) covalent geometry : angle 0.58346 (36916) *********************** 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 252 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6349 (m-90) cc_final: 0.6045 (m-90) REVERT: A 319 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6560 (ttt180) REVERT: A 759 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 960 ASN cc_start: 0.8325 (t0) cc_final: 0.7771 (m-40) REVERT: B 189 LEU cc_start: 0.6810 (pt) cc_final: 0.6355 (tt) REVERT: B 636 TYR cc_start: 0.5624 (m-10) cc_final: 0.5351 (m-10) REVERT: B 779 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7805 (mt0) REVERT: B 904 TYR cc_start: 0.6922 (m-10) cc_final: 0.6358 (m-10) REVERT: B 988 GLU cc_start: 0.7693 (pp20) cc_final: 0.7070 (tm-30) REVERT: C 235 ILE cc_start: 0.6701 (mm) cc_final: 0.6442 (mm) REVERT: C 266 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: C 424 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8210 (tttm) REVERT: C 906 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 960 ASN cc_start: 0.8533 (t0) cc_final: 0.7843 (m-40) outliers start: 75 outliers final: 42 residues processed: 231 average time/residue: 0.3328 time to fit residues: 129.2305 Evaluate side-chains 212 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 129 LYS 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 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 740 MET Chi-restraints excluded: chain B residue 759 PHE 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 266 TYR 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 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 0.0470 chunk 301 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 chunk 31 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN A1005 GLN B 148 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.185234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143694 restraints weight = 41860.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140454 restraints weight = 53468.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133137 restraints weight = 43516.594| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.070 27202 Z= 0.109 Angle : 0.683 37.680 37172 Z= 0.314 Chirality : 0.046 0.429 4359 Planarity : 0.004 0.051 4708 Dihedral : 7.099 86.580 4852 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 1.93 % Allowed : 15.60 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3273 helix: 1.45 (0.22), residues: 607 sheet: -0.10 (0.21), residues: 594 loop : -2.08 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.015 0.001 HIS B 49 PHE 0.022 0.001 PHE B 133 TYR 0.023 0.001 TYR C 453 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 51) link_NAG-ASN : angle 5.20059 ( 153) link_BETA1-4 : bond 0.00674 ( 9) link_BETA1-4 : angle 2.38259 ( 27) hydrogen bonds : bond 0.04138 ( 745) hydrogen bonds : angle 4.78231 ( 2070) SS BOND : bond 0.00328 ( 38) SS BOND : angle 1.83437 ( 76) covalent geometry : bond 0.00241 (27104) covalent geometry : angle 0.58855 (36916) *********************** 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 231 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6215 (m-90) cc_final: 0.5939 (m-90) REVERT: A 237 ARG cc_start: 0.7197 (ttt-90) cc_final: 0.6312 (tmt170) REVERT: A 239 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6388 (tp40) REVERT: A 319 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6580 (ttt180) REVERT: A 960 ASN cc_start: 0.8359 (t0) cc_final: 0.8103 (t0) REVERT: B 189 LEU cc_start: 0.7601 (pt) cc_final: 0.6809 (tt) REVERT: B 636 TYR cc_start: 0.5937 (m-10) cc_final: 0.5699 (m-10) REVERT: B 779 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7800 (mt0) REVERT: B 900 MET cc_start: 0.7549 (mtp) cc_final: 0.7281 (mtp) REVERT: B 904 TYR cc_start: 0.6808 (m-10) cc_final: 0.6303 (m-10) REVERT: B 988 GLU cc_start: 0.8102 (pp20) cc_final: 0.7423 (tm-30) REVERT: C 235 ILE cc_start: 0.6660 (mm) cc_final: 0.6281 (mm) REVERT: C 266 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: C 906 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8255 (t80) REVERT: C 960 ASN cc_start: 0.8475 (t0) cc_final: 0.7840 (m-40) outliers start: 55 outliers final: 38 residues processed: 218 average time/residue: 0.3736 time to fit residues: 138.5164 Evaluate side-chains 207 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 4.743 ------------------------------------------------------------------------------- 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 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 650 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 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 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 977 LEU 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 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 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 92 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 297 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 0.0870 chunk 236 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143231 restraints weight = 41268.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140120 restraints weight = 66373.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137715 restraints weight = 51240.834| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27202 Z= 0.109 Angle : 0.647 28.229 37172 Z= 0.304 Chirality : 0.046 0.374 4359 Planarity : 0.004 0.052 4708 Dihedral : 6.942 84.404 4852 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 2.28 % Allowed : 15.49 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3273 helix: 1.55 (0.22), residues: 601 sheet: -0.11 (0.20), residues: 605 loop : -2.06 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.012 0.001 HIS B 49 PHE 0.021 0.001 PHE A 238 TYR 0.021 0.001 TYR C 453 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 51) link_NAG-ASN : angle 4.34159 ( 153) link_BETA1-4 : bond 0.00641 ( 9) link_BETA1-4 : angle 2.28696 ( 27) hydrogen bonds : bond 0.04115 ( 745) hydrogen bonds : angle 4.72355 ( 2070) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.85687 ( 76) covalent geometry : bond 0.00245 (27104) covalent geometry : angle 0.57713 (36916) *********************** 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 241 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 176 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6813 (ttt180) REVERT: A 557 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6064 (pttp) REVERT: A 759 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.6610 (t80) REVERT: A 960 ASN cc_start: 0.8336 (t0) cc_final: 0.8043 (t0) REVERT: B 189 LEU cc_start: 0.6609 (pt) cc_final: 0.6176 (tt) REVERT: B 339 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6783 (t70) REVERT: B 636 TYR cc_start: 0.5322 (m-10) cc_final: 0.5111 (m-10) REVERT: B 779 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7755 (mt0) REVERT: B 900 MET cc_start: 0.7723 (mtp) cc_final: 0.7427 (mtp) REVERT: B 904 TYR cc_start: 0.6867 (m-10) cc_final: 0.6386 (m-10) REVERT: B 988 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: B 992 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7110 (mm110) REVERT: C 235 ILE cc_start: 0.6870 (mm) cc_final: 0.6644 (mm) REVERT: C 266 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: C 906 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8240 (t80) REVERT: C 960 ASN cc_start: 0.8520 (t0) cc_final: 0.7855 (m-40) outliers start: 65 outliers final: 45 residues processed: 224 average time/residue: 0.3825 time to fit residues: 143.0613 Evaluate side-chains 217 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 6.272 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 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 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 992 GLN 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 266 TYR 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 430 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 281 optimal weight: 0.3980 chunk 184 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.177049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144563 restraints weight = 41364.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140917 restraints weight = 65014.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137938 restraints weight = 52048.075| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3722 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= 0.102 Angle : 0.622 27.680 37172 Z= 0.294 Chirality : 0.046 0.369 4359 Planarity : 0.004 0.051 4708 Dihedral : 6.741 81.979 4852 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 2.00 % Allowed : 15.74 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3273 helix: 1.56 (0.22), residues: 608 sheet: -0.12 (0.21), residues: 570 loop : -2.00 (0.12), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.011 0.000 HIS B 49 PHE 0.021 0.001 PHE C 133 TYR 0.021 0.001 TYR C 453 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 51) link_NAG-ASN : angle 3.98583 ( 153) link_BETA1-4 : bond 0.00624 ( 9) link_BETA1-4 : angle 2.18138 ( 27) hydrogen bonds : bond 0.03796 ( 745) hydrogen bonds : angle 4.64194 ( 2070) SS BOND : bond 0.00264 ( 38) SS BOND : angle 1.08080 ( 76) covalent geometry : bond 0.00223 (27104) covalent geometry : angle 0.56326 (36916) *********************** 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 236 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6812 (ttt180) REVERT: A 557 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6052 (pttp) REVERT: A 759 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 960 ASN cc_start: 0.8304 (t0) cc_final: 0.8038 (t0) REVERT: A 1005 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8013 (tp40) REVERT: B 189 LEU cc_start: 0.6435 (pt) cc_final: 0.6019 (tt) REVERT: B 636 TYR cc_start: 0.5423 (m-10) cc_final: 0.5161 (m-10) REVERT: B 779 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7750 (mt0) REVERT: B 900 MET cc_start: 0.7552 (mtp) cc_final: 0.7246 (mtp) REVERT: B 904 TYR cc_start: 0.6692 (m-10) cc_final: 0.6217 (m-10) REVERT: B 988 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 992 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6987 (mm110) REVERT: C 266 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: C 906 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8195 (t80) REVERT: C 960 ASN cc_start: 0.8498 (t0) cc_final: 0.7848 (m-40) REVERT: C 981 LEU cc_start: 0.8581 (tp) cc_final: 0.8335 (tt) outliers start: 57 outliers final: 37 residues processed: 223 average time/residue: 0.3408 time to fit residues: 128.5454 Evaluate side-chains 209 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 906 PHE 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 313 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 263 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 325 optimal weight: 0.1980 chunk 265 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1005 GLN B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.175929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142962 restraints weight = 40946.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139596 restraints weight = 68662.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135824 restraints weight = 62012.925| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3813 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= 0.121 Angle : 0.642 24.588 37172 Z= 0.307 Chirality : 0.046 0.375 4359 Planarity : 0.004 0.051 4708 Dihedral : 6.724 81.680 4852 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.51 % Rotamer: Outliers : 1.72 % Allowed : 16.30 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3273 helix: 1.46 (0.22), residues: 613 sheet: -0.12 (0.21), residues: 568 loop : -1.99 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.010 0.001 HIS B 49 PHE 0.040 0.001 PHE C 133 TYR 0.020 0.001 TYR B 495 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 51) link_NAG-ASN : angle 3.82652 ( 153) link_BETA1-4 : bond 0.00640 ( 9) link_BETA1-4 : angle 2.17548 ( 27) hydrogen bonds : bond 0.04173 ( 745) hydrogen bonds : angle 4.66596 ( 2070) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.92372 ( 76) covalent geometry : bond 0.00281 (27104) covalent geometry : angle 0.58629 (36916) ********************** 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 214 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7464 (tmt170) cc_final: 0.7130 (tmt170) REVERT: A 239 GLN cc_start: 0.6837 (tp-100) cc_final: 0.6633 (tp40) REVERT: A 319 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6794 (ttt180) REVERT: A 557 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6128 (pttp) REVERT: A 759 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.6512 (t80) REVERT: A 960 ASN cc_start: 0.8357 (t0) cc_final: 0.8084 (t0) REVERT: B 636 TYR cc_start: 0.5456 (m-10) cc_final: 0.5149 (m-10) REVERT: B 900 MET cc_start: 0.7588 (mtp) cc_final: 0.7273 (mtp) REVERT: B 904 TYR cc_start: 0.6852 (m-10) cc_final: 0.6326 (m-10) REVERT: B 988 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: B 992 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7058 (mm110) REVERT: C 266 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: C 906 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8182 (t80) REVERT: C 960 ASN cc_start: 0.8547 (t0) cc_final: 0.7877 (m-40) REVERT: C 981 LEU cc_start: 0.8596 (tp) cc_final: 0.8367 (tt) outliers start: 49 outliers final: 38 residues processed: 204 average time/residue: 0.3952 time to fit residues: 137.6327 Evaluate side-chains 204 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 992 GLN 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 266 TYR 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 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 chunk 299 optimal weight: 0.0870 chunk 252 optimal weight: 6.9990 chunk 306 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 0.0000 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4157 r_free = 0.4157 target = 0.172237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143358 restraints weight = 42119.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139454 restraints weight = 71341.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137410 restraints weight = 63157.186| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 27202 Z= 0.106 Angle : 0.618 23.246 37172 Z= 0.296 Chirality : 0.046 0.383 4359 Planarity : 0.004 0.051 4708 Dihedral : 6.550 79.212 4852 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.58 % Rotamer: Outliers : 1.76 % Allowed : 16.40 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3273 helix: 1.52 (0.22), residues: 620 sheet: -0.00 (0.21), residues: 573 loop : -1.99 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.010 0.000 HIS B 49 PHE 0.023 0.001 PHE C 392 TYR 0.021 0.001 TYR C 453 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 51) link_NAG-ASN : angle 3.74200 ( 153) link_BETA1-4 : bond 0.00598 ( 9) link_BETA1-4 : angle 2.11666 ( 27) hydrogen bonds : bond 0.03831 ( 745) hydrogen bonds : angle 4.62850 ( 2070) SS BOND : bond 0.00252 ( 38) SS BOND : angle 1.15220 ( 76) covalent geometry : bond 0.00242 (27104) covalent geometry : angle 0.56650 (36916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9339.22 seconds wall clock time: 167 minutes 45.65 seconds (10065.65 seconds total)