Starting phenix.real_space_refine on Sun Jul 5 05:32:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p99_17576/07_2026/8p99_17576.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 114 5.16 5 C 16372 2.51 5 N 4224 2.21 5 O 5003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25713 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8354 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8369 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 1019} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8374 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 54, 'TRANS': 1021} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.08, per 1000 atoms: 0.20 Number of scatterers: 25713 At special positions: 0 Unit cell: (148.77, 159.03, 194.085, 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 114 16.00 O 5003 8.00 N 4224 7.00 C 16372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.97 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.94 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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=2.79 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.08 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=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.78 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.95 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.87 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.00 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.98 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.93 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.06 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=1.99 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.10 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.11 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.87 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.11 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.98 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.00 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.88 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.74 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=1.91 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=8, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 164 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 343 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 343 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 282 " " NAG P 1 " - " ASN C 343 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.563A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.569A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.739A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.655A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.320A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.015A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.127A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.006A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.577A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.613A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.084A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.769A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.875A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.530A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.575A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.009A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 829 removed outlier: 3.592A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.767A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.028A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 966 removed outlier: 3.683A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.658A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.957A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.250A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.392A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.116A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.811A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.630A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.663A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.522A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.830A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.555A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.036A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.626A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.720A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.784A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.889A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.038A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.134A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.655A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.798A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.964A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.618A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.054A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.682A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.387A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.917A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.838A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 6.811A pdb=" N ALA A1080 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1095 through 1097 removed outlier: 3.639A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.790A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.641A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.776A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.715A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.275A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.266A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 4.141A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.632A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.675A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.568A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 6.504A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1096 removed outlier: 3.651A pdb=" N GLN B1113 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.356A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.828A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.577A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.125A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.684A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.468A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.897A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.183A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.847A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.997A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.695A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 1 1.03 - 1.24: 3586 1.24 - 1.46: 9572 1.46 - 1.67: 12998 1.67 - 1.89: 144 Bond restraints: 26301 Sorted by residual: bond pdb=" C ASP A1146 " pdb=" O ASP A1146 " ideal model delta sigma weight residual 1.231 1.865 -0.634 2.00e-02 2.50e+03 1.00e+03 bond pdb=" C ASP B1146 " pdb=" O ASP B1146 " ideal model delta sigma weight residual 1.231 0.810 0.421 2.00e-02 2.50e+03 4.44e+02 bond pdb=" C ASP C1146 " pdb=" O ASP C1146 " ideal model delta sigma weight residual 1.231 1.609 -0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" N PHE A 338 " pdb=" CA PHE A 338 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.28e-02 6.10e+03 5.60e+01 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.237 1.157 0.079 1.17e-02 7.31e+03 4.60e+01 ... (remaining 26296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.84: 35650 6.84 - 13.68: 143 13.68 - 20.52: 10 20.52 - 27.36: 2 27.36 - 34.19: 3 Bond angle restraints: 35808 Sorted by residual: angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.84 154.03 -34.19 1.25e+00 6.40e-01 7.48e+02 angle pdb=" CA ASP A1146 " pdb=" C ASP A1146 " pdb=" O ASP A1146 " ideal model delta sigma weight residual 120.80 86.64 34.16 1.70e+00 3.46e-01 4.04e+02 angle pdb=" C LYS A 462 " pdb=" N PRO A 463 " pdb=" CA PRO A 463 " ideal model delta sigma weight residual 119.76 105.62 14.14 1.03e+00 9.43e-01 1.88e+02 angle pdb=" CA ASP B1146 " pdb=" C ASP B1146 " pdb=" O ASP B1146 " ideal model delta sigma weight residual 120.80 142.51 -21.71 1.70e+00 3.46e-01 1.63e+02 angle pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" O CYS B 617 " ideal model delta sigma weight residual 119.97 105.49 14.48 1.15e+00 7.56e-01 1.59e+02 ... (remaining 35803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 13771 17.25 - 34.51: 1175 34.51 - 51.76: 257 51.76 - 69.01: 67 69.01 - 86.26: 17 Dihedral angle restraints: 15287 sinusoidal: 5920 harmonic: 9367 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.61 -79.39 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" C LEU B 335 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " pdb=" CB LEU B 335 " ideal model delta harmonic sigma weight residual -122.60 -136.70 14.10 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -40.27 -45.73 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 15284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.781: 4179 0.781 - 1.563: 1 1.563 - 2.344: 0 2.344 - 3.126: 0 3.126 - 3.907: 1 Chirality restraints: 4181 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 1.51 -3.91 2.00e-01 2.50e+01 3.82e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.77e+01 ... (remaining 4178 not shown) Planarity restraints: 4618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 347 " -0.025 2.00e-02 2.50e+03 6.37e-02 7.10e+01 pdb=" CG PHE C 347 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 347 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE C 347 " 0.100 2.00e-02 2.50e+03 pdb=" CE1 PHE C 347 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 PHE C 347 " -0.108 2.00e-02 2.50e+03 pdb=" CZ PHE C 347 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 940 " -0.032 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C SER B 940 " 0.113 2.00e-02 2.50e+03 pdb=" O SER B 940 " -0.043 2.00e-02 2.50e+03 pdb=" N THR B 941 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 643 " 0.048 2.00e-02 2.50e+03 3.97e-02 2.76e+01 pdb=" CG PHE B 643 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 643 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE B 643 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 643 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 643 " -0.033 2.00e-02 2.50e+03 pdb=" CZ PHE B 643 " 0.070 2.00e-02 2.50e+03 ... (remaining 4615 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 42 1.90 - 2.65: 928 2.65 - 3.40: 36295 3.40 - 4.15: 59172 4.15 - 4.90: 104025 Nonbonded interactions: 200462 Sorted by model distance: nonbonded pdb=" CG2 THR A1116 " pdb=" CB TYR A1138 " model vdw 1.154 3.860 nonbonded pdb=" OH TYR A 37 " pdb=" NZ LYS A 195 " model vdw 1.204 3.120 nonbonded pdb=" OE2 GLU C 725 " pdb=" NZ LYS C1028 " model vdw 1.260 3.120 nonbonded pdb=" NZ LYS B 310 " pdb=" OD2 ASP B 663 " model vdw 1.299 3.120 nonbonded pdb=" N GLN B 115 " pdb=" OE2 GLU B 132 " model vdw 1.304 3.120 ... (remaining 200457 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 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 515 or resid 523 through 579 or \ (resid 580 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 1 through 616 or (resid 617 and (name N or name CA or name C or name CB or name \ SG )) or resid 618 through 939 or (resid 940 through 944 and (name N or name CA \ or name C or name O or name CB )) or resid 945 through 1307)) selection = (chain 'B' and (resid 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 616 or (resid 617 and (name N o \ r name CA or name C or name CB or name SG )) or resid 618 through 621 or resid 6 \ 41 through 827 or resid 854 through 939 or (resid 940 through 944 and (name N or \ name CA or name C or name O or name CB )) or resid 945 through 1307)) selection = (chain 'C' and (resid 15 through 515 or resid 523 through 579 or (resid 580 and \ (name N or name CA or name C or name O or name CB )) or resid 581 through 827 or \ resid 854 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.680 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.017 0.944 26387 Z= 1.068 Angle : 1.700 43.474 36005 Z= 1.038 Chirality : 0.112 3.907 4181 Planarity : 0.007 0.066 4587 Dihedral : 13.576 86.262 9154 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 60.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 8.63 % Allowed : 11.35 % Favored : 80.02 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3187 helix: 3.29 (0.18), residues: 646 sheet: 1.41 (0.21), residues: 635 loop : -0.84 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG C 355 TYR 0.059 0.005 TYR A 741 PHE 0.108 0.006 PHE C 347 TRP 0.067 0.006 TRP B1102 HIS 0.046 0.006 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01239 / 0.76 (26301) covalent geometry : angle 1.53289 / 0.99 (35808) SS BOND : bond 0.25697 / 17.45 ( 37) SS BOND : angle 14.28561 / 10.75 ( 74) hydrogen bonds : bond 0.25311 / 16.85 ( 873) hydrogen bonds : angle 8.71340 / 6.02 ( 2463) Misc. bond : bond 0.33310 / 20.97 ( 8) link_BETA1-4 : bond 0.00539 / 0.44 ( 10) link_BETA1-4 : angle 2.39703 / 1.60 ( 30) link_NAG-ASN : bond 0.00953 / 0.62 ( 31) link_NAG-ASN : angle 7.09125 / 4.66 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 834 time to evaluate : 0.927 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8473 (t) cc_final: 0.8105 (m) REVERT: A 200 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: A 228 ASP cc_start: 0.7936 (m-30) cc_final: 0.7538 (t0) REVERT: A 298 GLU cc_start: 0.6753 (tt0) cc_final: 0.6492 (tt0) REVERT: A 317 ASN cc_start: 0.7320 (m-40) cc_final: 0.6499 (m-40) REVERT: A 321 GLN cc_start: 0.7483 (mm110) cc_final: 0.7190 (mm110) REVERT: A 418 ILE cc_start: 0.7785 (tt) cc_final: 0.7478 (tt) REVERT: A 465 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: A 610 VAL cc_start: 0.8445 (t) cc_final: 0.8237 (p) REVERT: A 671 CYS cc_start: 0.5618 (m) cc_final: 0.5361 (m) REVERT: A 708 SER cc_start: 0.7546 (t) cc_final: 0.7212 (m) REVERT: A 822 LEU cc_start: 0.8520 (mt) cc_final: 0.8305 (mt) REVERT: A 900 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6767 (mtt) REVERT: A 980 ILE cc_start: 0.8209 (mm) cc_final: 0.7926 (mt) REVERT: A 1004 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7947 (tt) REVERT: A 1029 MET cc_start: 0.7895 (mmm) cc_final: 0.7687 (tpt) REVERT: A 1096 VAL cc_start: 0.8256 (m) cc_final: 0.8021 (t) REVERT: A 1113 GLN cc_start: 0.7325 (mt0) cc_final: 0.6923 (mt0) REVERT: B 46 SER cc_start: 0.7971 (m) cc_final: 0.7694 (t) REVERT: B 52 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 54 LEU cc_start: 0.8376 (mp) cc_final: 0.8052 (mt) REVERT: B 55 PHE cc_start: 0.6843 (m-80) cc_final: 0.6542 (m-10) REVERT: B 61 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6227 (p0) REVERT: B 92 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 122 ASN cc_start: 0.2368 (OUTLIER) cc_final: 0.2029 (t0) REVERT: B 170 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7352 (t80) REVERT: B 191 GLU cc_start: 0.6092 (mp0) cc_final: 0.5802 (mp0) REVERT: B 193 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7618 (m) REVERT: B 205 SER cc_start: 0.8100 (t) cc_final: 0.7879 (p) REVERT: B 274 THR cc_start: 0.6330 (m) cc_final: 0.6115 (m) REVERT: B 278 LYS cc_start: 0.8195 (tttm) cc_final: 0.7990 (tttm) REVERT: B 281 GLU cc_start: 0.6815 (tp30) cc_final: 0.6578 (tp30) REVERT: B 539 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6614 (t) REVERT: B 578 ASP cc_start: 0.7321 (p0) cc_final: 0.7024 (p0) REVERT: B 581 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6803 (p) REVERT: B 584 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7158 (mp) REVERT: B 716 THR cc_start: 0.7718 (p) cc_final: 0.7355 (m) REVERT: B 864 LEU cc_start: 0.8039 (tp) cc_final: 0.7503 (tp) REVERT: B 992 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: B 1023 ASN cc_start: 0.7609 (m-40) cc_final: 0.7327 (m-40) REVERT: B 1086 LYS cc_start: 0.7789 (mtmt) cc_final: 0.7343 (mtmt) REVERT: B 1117 THR cc_start: 0.8059 (m) cc_final: 0.7699 (p) REVERT: C 46 SER cc_start: 0.7893 (m) cc_final: 0.7629 (p) REVERT: C 63 THR cc_start: 0.6928 (OUTLIER) cc_final: 0.6370 (p) REVERT: C 105 ILE cc_start: 0.7652 (mp) cc_final: 0.7123 (mt) REVERT: C 120 VAL cc_start: 0.7992 (t) cc_final: 0.7750 (m) REVERT: C 221 SER cc_start: 0.8181 (m) cc_final: 0.7960 (p) REVERT: C 231 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6603 (mp) REVERT: C 355 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6390 (ttp-110) REVERT: C 377 PHE cc_start: 0.7930 (t80) cc_final: 0.7448 (t80) REVERT: C 492 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6721 (pt) REVERT: C 505 TYR cc_start: 0.7122 (t80) cc_final: 0.6756 (t80) REVERT: C 513 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7645 (mt) REVERT: C 588 THR cc_start: 0.8337 (m) cc_final: 0.7884 (p) REVERT: C 642 VAL cc_start: 0.8276 (m) cc_final: 0.8035 (t) REVERT: C 660 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: C 692 ILE cc_start: 0.8210 (mp) cc_final: 0.7758 (mt) REVERT: C 704 SER cc_start: 0.8556 (t) cc_final: 0.8204 (p) REVERT: C 707 TYR cc_start: 0.7671 (t80) cc_final: 0.7193 (t80) REVERT: C 716 THR cc_start: 0.7930 (p) cc_final: 0.7601 (t) REVERT: C 748 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6350 (mt-10) REVERT: C 752 LEU cc_start: 0.7717 (mp) cc_final: 0.7033 (mt) REVERT: C 755 GLN cc_start: 0.6954 (mt0) cc_final: 0.6595 (mt0) REVERT: C 823 PHE cc_start: 0.7356 (t80) cc_final: 0.7098 (t80) REVERT: C 884 SER cc_start: 0.8594 (m) cc_final: 0.8356 (p) REVERT: C 900 MET cc_start: 0.7653 (mtp) cc_final: 0.7374 (mtp) REVERT: C 981 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7370 (mp) REVERT: C 990 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6582 (mm-30) REVERT: C 1000 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7382 (mtt180) REVERT: C 1045 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7815 (mmmt) outliers start: 241 outliers final: 126 residues processed: 1006 average time/residue: 0.1653 time to fit residues: 263.8659 Evaluate side-chains 878 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 732 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 164 ASN A 317 ASN A 321 GLN A 370 ASN A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 613 GLN A 641 ASN A 675 GLN A 690 GLN A 751 ASN A 755 GLN A 762 GLN A 787 GLN A 965 GLN A 969 ASN A1010 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1108 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 122 ASN B 211 ASN B 218 GLN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 501 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 606 ASN B 641 ASN B 675 GLN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 125 ASN C 239 GLN C 314 GLN C 388 ASN C 394 ASN C 409 GLN C 414 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 563 GLN C 603 ASN C 703 ASN C 751 ASN C 779 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1125 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.168226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138327 restraints weight = 41151.867| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.01 r_work: 0.3553 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 26387 Z= 0.194 Angle : 0.838 16.272 36005 Z= 0.417 Chirality : 0.054 0.819 4181 Planarity : 0.005 0.076 4587 Dihedral : 9.478 78.915 3757 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.13 % Favored : 97.74 % Rotamer: Outliers : 6.59 % Allowed : 16.58 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3187 helix: 2.56 (0.19), residues: 665 sheet: 1.18 (0.20), residues: 648 loop : -1.04 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 237 TYR 0.028 0.002 TYR B 265 PHE 0.038 0.003 PHE C 497 TRP 0.036 0.002 TRP A 64 HIS 0.012 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (26301) covalent geometry : angle 0.80149 / 0.41 (35808) SS BOND : bond 0.00453 / 0.29 ( 37) SS BOND : angle 2.25437 / 1.55 ( 74) hydrogen bonds : bond 0.05800 / 3.79 ( 873) hydrogen bonds : angle 6.67780 / 4.60 ( 2463) Misc. bond : bond 0.00613 / 0.35 ( 8) link_BETA1-4 : bond 0.00497 / 0.38 ( 10) link_BETA1-4 : angle 1.56437 / 1.04 ( 30) link_NAG-ASN : bond 0.00642 / 0.42 ( 31) link_NAG-ASN : angle 4.47492 / 3.06 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 748 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7899 (t) cc_final: 0.6584 (p) REVERT: A 30 ASN cc_start: 0.8313 (t0) cc_final: 0.8053 (t0) REVERT: A 53 ASP cc_start: 0.7399 (t0) cc_final: 0.6982 (t0) REVERT: A 169 GLU cc_start: 0.7558 (mp0) cc_final: 0.7333 (mp0) REVERT: A 191 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 200 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: A 299 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 309 GLU cc_start: 0.7742 (mp0) cc_final: 0.7386 (mp0) REVERT: A 378 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7259 (mtpt) REVERT: A 389 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7400 (t0) REVERT: A 453 TYR cc_start: 0.7944 (p90) cc_final: 0.6165 (p90) REVERT: A 465 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 493 GLN cc_start: 0.7657 (tp40) cc_final: 0.7402 (tm-30) REVERT: A 564 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7001 (mm-40) REVERT: A 578 ASP cc_start: 0.7731 (t70) cc_final: 0.7399 (t70) REVERT: A 596 SER cc_start: 0.8570 (m) cc_final: 0.7904 (p) REVERT: A 651 ILE cc_start: 0.8399 (mt) cc_final: 0.8049 (mm) REVERT: A 693 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8500 (pt) REVERT: A 708 SER cc_start: 0.7959 (t) cc_final: 0.7625 (m) REVERT: A 737 ASP cc_start: 0.8078 (t0) cc_final: 0.7670 (t0) REVERT: A 781 VAL cc_start: 0.8287 (p) cc_final: 0.8013 (t) REVERT: A 896 ILE cc_start: 0.8452 (mt) cc_final: 0.8179 (tt) REVERT: A 900 MET cc_start: 0.7780 (mtt) cc_final: 0.7284 (mtm) REVERT: A 980 ILE cc_start: 0.8363 (mm) cc_final: 0.8122 (mt) REVERT: A 983 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8196 (ttt180) REVERT: A 1004 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8095 (tt) REVERT: A 1019 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7431 (tpp80) REVERT: A 1033 VAL cc_start: 0.8583 (t) cc_final: 0.8283 (p) REVERT: A 1065 VAL cc_start: 0.8315 (m) cc_final: 0.8046 (p) REVERT: A 1072 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: A 1092 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: A 1113 GLN cc_start: 0.7847 (mt0) cc_final: 0.7645 (mt0) REVERT: A 1119 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7244 (t0) REVERT: A 1123 SER cc_start: 0.8813 (t) cc_final: 0.8540 (p) REVERT: B 46 SER cc_start: 0.8388 (m) cc_final: 0.8106 (t) REVERT: B 52 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 54 LEU cc_start: 0.8541 (mp) cc_final: 0.8333 (mt) REVERT: B 61 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.5592 (p0) REVERT: B 105 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (mt) REVERT: B 193 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.7765 (m) REVERT: B 270 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 274 THR cc_start: 0.8059 (m) cc_final: 0.7718 (p) REVERT: B 577 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7683 (ttm-80) REVERT: B 663 ASP cc_start: 0.7431 (t0) cc_final: 0.7148 (t0) REVERT: B 673 SER cc_start: 0.8647 (t) cc_final: 0.8360 (p) REVERT: B 716 THR cc_start: 0.8291 (p) cc_final: 0.7925 (t) REVERT: B 725 GLU cc_start: 0.7558 (tt0) cc_final: 0.7085 (tt0) REVERT: B 742 ILE cc_start: 0.8516 (mt) cc_final: 0.8286 (mt) REVERT: B 752 LEU cc_start: 0.8531 (mm) cc_final: 0.8194 (mt) REVERT: B 763 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 779 GLN cc_start: 0.8089 (tp40) cc_final: 0.7739 (tp40) REVERT: B 789 TYR cc_start: 0.7177 (m-80) cc_final: 0.6974 (m-10) REVERT: B 819 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 823 PHE cc_start: 0.7408 (m-80) cc_final: 0.7074 (m-10) REVERT: B 864 LEU cc_start: 0.8260 (tp) cc_final: 0.7657 (tp) REVERT: B 902 MET cc_start: 0.7800 (tpt) cc_final: 0.7576 (tpt) REVERT: B 965 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8295 (mm110) REVERT: B 975 SER cc_start: 0.8777 (p) cc_final: 0.8542 (m) REVERT: B 979 ASP cc_start: 0.7722 (t0) cc_final: 0.7367 (t0) REVERT: B 985 ASP cc_start: 0.7509 (p0) cc_final: 0.7138 (p0) REVERT: B 1023 ASN cc_start: 0.8096 (m-40) cc_final: 0.7854 (m-40) REVERT: B 1028 LYS cc_start: 0.8141 (tppt) cc_final: 0.7723 (tttt) REVERT: B 1045 LYS cc_start: 0.8138 (tttm) cc_final: 0.7887 (tttm) REVERT: B 1050 MET cc_start: 0.8585 (ptp) cc_final: 0.8372 (ptp) REVERT: B 1084 ASP cc_start: 0.7559 (p0) cc_final: 0.6451 (p0) REVERT: B 1086 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7552 (mtmt) REVERT: B 1114 ILE cc_start: 0.8161 (mp) cc_final: 0.7886 (tp) REVERT: C 46 SER cc_start: 0.8210 (m) cc_final: 0.7865 (p) REVERT: C 51 THR cc_start: 0.8338 (m) cc_final: 0.7923 (p) REVERT: C 63 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6119 (p) REVERT: C 88 ASP cc_start: 0.7884 (p0) cc_final: 0.7576 (p0) REVERT: C 120 VAL cc_start: 0.8190 (t) cc_final: 0.7953 (m) REVERT: C 205 SER cc_start: 0.8558 (m) cc_final: 0.8194 (p) REVERT: C 221 SER cc_start: 0.8328 (m) cc_final: 0.7933 (p) REVERT: C 378 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7421 (ptpt) REVERT: C 380 TYR cc_start: 0.7653 (m-10) cc_final: 0.7251 (m-10) REVERT: C 492 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7534 (pt) REVERT: C 505 TYR cc_start: 0.7350 (t80) cc_final: 0.6852 (t80) REVERT: C 535 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7845 (mtpp) REVERT: C 578 ASP cc_start: 0.7506 (t0) cc_final: 0.7293 (t0) REVERT: C 692 ILE cc_start: 0.8289 (mp) cc_final: 0.8007 (mt) REVERT: C 707 TYR cc_start: 0.8009 (t80) cc_final: 0.7588 (t80) REVERT: C 748 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7133 (mt-10) REVERT: C 805 ILE cc_start: 0.7960 (mm) cc_final: 0.7690 (mt) REVERT: C 821 LEU cc_start: 0.8296 (tp) cc_final: 0.8032 (mt) REVERT: C 884 SER cc_start: 0.8652 (m) cc_final: 0.8374 (p) REVERT: C 900 MET cc_start: 0.7888 (mtp) cc_final: 0.7530 (mtp) REVERT: C 905 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7930 (mtt180) REVERT: C 949 GLN cc_start: 0.8081 (tp40) cc_final: 0.7781 (mm-40) REVERT: C 964 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8493 (ttmm) REVERT: C 981 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 990 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 1000 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7870 (mtt180) REVERT: C 1019 ARG cc_start: 0.8327 (ttt-90) cc_final: 0.8091 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8190 (mmmt) REVERT: C 1086 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8035 (ttmm) REVERT: C 1115 ILE cc_start: 0.8693 (mt) cc_final: 0.8421 (mm) outliers start: 184 outliers final: 88 residues processed: 858 average time/residue: 0.1649 time to fit residues: 223.7625 Evaluate side-chains 798 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 693 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 169 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 137 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 101 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 777 ASN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136376 restraints weight = 40872.292| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.00 r_work: 0.3508 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26387 Z= 0.179 Angle : 0.726 16.137 36005 Z= 0.359 Chirality : 0.050 0.552 4181 Planarity : 0.005 0.056 4587 Dihedral : 7.537 61.357 3571 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 5.80 % Allowed : 18.58 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3187 helix: 2.24 (0.19), residues: 665 sheet: 0.86 (0.20), residues: 637 loop : -1.09 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.022 0.002 TYR C 396 PHE 0.027 0.002 PHE B 592 TRP 0.017 0.002 TRP C 436 HIS 0.010 0.002 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (26301) covalent geometry : angle 0.69900 / 0.35 (35808) SS BOND : bond 0.00464 / 0.28 ( 37) SS BOND : angle 1.88443 / 1.30 ( 74) hydrogen bonds : bond 0.04901 / 3.19 ( 873) hydrogen bonds : angle 6.12035 / 4.20 ( 2463) Misc. bond : bond 0.00348 / 0.18 ( 8) link_BETA1-4 : bond 0.00289 / 0.22 ( 10) link_BETA1-4 : angle 1.25044 / 0.86 ( 30) link_NAG-ASN : bond 0.00537 / 0.34 ( 31) link_NAG-ASN : angle 3.55167 / 2.32 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 717 time to evaluate : 0.924 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7835 (t) cc_final: 0.6593 (p) REVERT: A 30 ASN cc_start: 0.8369 (t0) cc_final: 0.8067 (t0) REVERT: A 53 ASP cc_start: 0.7497 (t0) cc_final: 0.7061 (t0) REVERT: A 200 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: A 287 ASP cc_start: 0.7458 (t0) cc_final: 0.7107 (m-30) REVERT: A 309 GLU cc_start: 0.7685 (mp0) cc_final: 0.7311 (mp0) REVERT: A 386 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7424 (mttt) REVERT: A 394 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (t0) REVERT: A 453 TYR cc_start: 0.7827 (p90) cc_final: 0.6546 (p90) REVERT: A 465 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: A 564 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6980 (mm-40) REVERT: A 578 ASP cc_start: 0.7747 (t70) cc_final: 0.7525 (t0) REVERT: A 595 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8379 (p) REVERT: A 596 SER cc_start: 0.8627 (m) cc_final: 0.8257 (p) REVERT: A 651 ILE cc_start: 0.8386 (mt) cc_final: 0.8084 (mm) REVERT: A 693 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (pt) REVERT: A 708 SER cc_start: 0.8008 (t) cc_final: 0.7739 (m) REVERT: A 737 ASP cc_start: 0.8090 (t0) cc_final: 0.7676 (t0) REVERT: A 781 VAL cc_start: 0.8299 (p) cc_final: 0.8003 (t) REVERT: A 819 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 896 ILE cc_start: 0.8452 (mt) cc_final: 0.8189 (tt) REVERT: A 900 MET cc_start: 0.7795 (mtt) cc_final: 0.7300 (mtm) REVERT: A 964 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8423 (ttmp) REVERT: A 1019 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7433 (tpp80) REVERT: A 1065 VAL cc_start: 0.8423 (m) cc_final: 0.8051 (p) REVERT: B 46 SER cc_start: 0.8464 (m) cc_final: 0.8234 (t) REVERT: B 52 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 54 LEU cc_start: 0.8697 (mp) cc_final: 0.8266 (mt) REVERT: B 117 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7229 (tt) REVERT: B 132 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5846 (mm-30) REVERT: B 193 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.7796 (m) REVERT: B 195 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7827 (ttmm) REVERT: B 270 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7328 (mp) REVERT: B 274 THR cc_start: 0.8019 (m) cc_final: 0.7637 (p) REVERT: B 335 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7810 (tt) REVERT: B 599 THR cc_start: 0.8132 (m) cc_final: 0.7807 (t) REVERT: B 615 VAL cc_start: 0.8663 (t) cc_final: 0.8461 (t) REVERT: B 663 ASP cc_start: 0.7567 (t0) cc_final: 0.7232 (t0) REVERT: B 673 SER cc_start: 0.8707 (t) cc_final: 0.8479 (p) REVERT: B 725 GLU cc_start: 0.7538 (tt0) cc_final: 0.7090 (tt0) REVERT: B 752 LEU cc_start: 0.8618 (mm) cc_final: 0.8299 (mt) REVERT: B 773 GLU cc_start: 0.7506 (tp30) cc_final: 0.7303 (tp30) REVERT: B 779 GLN cc_start: 0.8148 (tp40) cc_final: 0.7880 (tp40) REVERT: B 819 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7012 (mt-10) REVERT: B 902 MET cc_start: 0.7881 (tpt) cc_final: 0.7535 (tpt) REVERT: B 965 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8308 (mm110) REVERT: B 979 ASP cc_start: 0.7652 (t0) cc_final: 0.7267 (t0) REVERT: B 985 ASP cc_start: 0.7407 (p0) cc_final: 0.7108 (p0) REVERT: B 1019 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7415 (ttp80) REVERT: B 1023 ASN cc_start: 0.8134 (m-40) cc_final: 0.7864 (m-40) REVERT: B 1028 LYS cc_start: 0.8191 (tppt) cc_final: 0.7735 (tttt) REVERT: B 1029 MET cc_start: 0.7995 (tpp) cc_final: 0.7664 (ttp) REVERT: B 1043 CYS cc_start: 0.6308 (OUTLIER) cc_final: 0.6012 (m) REVERT: B 1045 LYS cc_start: 0.8240 (tttm) cc_final: 0.7922 (tttm) REVERT: B 1050 MET cc_start: 0.8532 (ptp) cc_final: 0.8320 (ptp) REVERT: B 1084 ASP cc_start: 0.7434 (p0) cc_final: 0.6189 (p0) REVERT: B 1086 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7616 (mtmt) REVERT: B 1114 ILE cc_start: 0.8116 (mp) cc_final: 0.7915 (tp) REVERT: C 46 SER cc_start: 0.8217 (m) cc_final: 0.7886 (p) REVERT: C 63 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6227 (t) REVERT: C 120 VAL cc_start: 0.8187 (t) cc_final: 0.7644 (m) REVERT: C 127 VAL cc_start: 0.8490 (t) cc_final: 0.8062 (p) REVERT: C 153 MET cc_start: -0.1854 (ptt) cc_final: -0.2066 (ptt) REVERT: C 205 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8164 (p) REVERT: C 231 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6493 (pt) REVERT: C 294 ASP cc_start: 0.7540 (p0) cc_final: 0.7330 (p0) REVERT: C 317 ASN cc_start: 0.7679 (m-40) cc_final: 0.6941 (m-40) REVERT: C 319 ARG cc_start: 0.7768 (ptt-90) cc_final: 0.7568 (ptt-90) REVERT: C 340 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 378 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7516 (ptpt) REVERT: C 380 TYR cc_start: 0.7597 (m-10) cc_final: 0.7259 (m-10) REVERT: C 394 ASN cc_start: 0.7788 (t0) cc_final: 0.7318 (t0) REVERT: C 396 TYR cc_start: 0.7854 (m-10) cc_final: 0.7615 (m-80) REVERT: C 492 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (pt) REVERT: C 535 LYS cc_start: 0.8224 (mtpp) cc_final: 0.8013 (mtpp) REVERT: C 578 ASP cc_start: 0.7482 (t0) cc_final: 0.7249 (t0) REVERT: C 619 GLU cc_start: 0.7568 (tp30) cc_final: 0.7337 (tt0) REVERT: C 661 GLU cc_start: 0.7294 (pm20) cc_final: 0.6896 (pm20) REVERT: C 707 TYR cc_start: 0.7983 (t80) cc_final: 0.7651 (t80) REVERT: C 748 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7163 (mt-10) REVERT: C 752 LEU cc_start: 0.8713 (mt) cc_final: 0.8365 (mt) REVERT: C 884 SER cc_start: 0.8673 (m) cc_final: 0.8393 (p) REVERT: C 887 THR cc_start: 0.8491 (m) cc_final: 0.8135 (p) REVERT: C 900 MET cc_start: 0.7905 (mtp) cc_final: 0.7467 (mtt) REVERT: C 949 GLN cc_start: 0.8102 (tp40) cc_final: 0.7790 (mm-40) REVERT: C 981 LEU cc_start: 0.8671 (mp) cc_final: 0.8042 (mp) REVERT: C 1000 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7861 (mtt180) REVERT: C 1019 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.8014 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8301 (mmmm) REVERT: C 1072 GLU cc_start: 0.7941 (pm20) cc_final: 0.7614 (pm20) REVERT: C 1118 ASP cc_start: 0.7218 (p0) cc_final: 0.6959 (p0) outliers start: 162 outliers final: 94 residues processed: 816 average time/residue: 0.1591 time to fit residues: 205.9651 Evaluate side-chains 790 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 679 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 93 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 304 optimal weight: 0.1980 chunk 195 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 278 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134843 restraints weight = 40725.760| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.12 r_work: 0.3492 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26387 Z= 0.183 Angle : 0.697 15.831 36005 Z= 0.343 Chirality : 0.048 0.501 4181 Planarity : 0.005 0.068 4587 Dihedral : 7.120 63.561 3547 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 5.84 % Allowed : 19.84 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3187 helix: 2.13 (0.20), residues: 662 sheet: 0.66 (0.20), residues: 656 loop : -1.15 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.022 0.002 TYR C 505 PHE 0.025 0.002 PHE C 168 TRP 0.032 0.002 TRP A 64 HIS 0.008 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (26301) covalent geometry : angle 0.67346 / 0.34 (35808) SS BOND : bond 0.00463 / 0.30 ( 37) SS BOND : angle 1.74348 / 1.17 ( 74) hydrogen bonds : bond 0.04513 / 2.96 ( 873) hydrogen bonds : angle 5.87629 / 4.04 ( 2463) Misc. bond : bond 0.00517 / 0.27 ( 8) link_BETA1-4 : bond 0.00285 / 0.21 ( 10) link_BETA1-4 : angle 1.15402 / 0.78 ( 30) link_NAG-ASN : bond 0.00529 / 0.33 ( 31) link_NAG-ASN : angle 3.26968 / 2.12 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 706 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7708 (t) cc_final: 0.6372 (p) REVERT: A 30 ASN cc_start: 0.8355 (t0) cc_final: 0.8002 (t0) REVERT: A 53 ASP cc_start: 0.7528 (t0) cc_final: 0.7106 (t0) REVERT: A 60 SER cc_start: 0.8404 (t) cc_final: 0.8151 (m) REVERT: A 177 MET cc_start: -0.2136 (mtp) cc_final: -0.2387 (mtt) REVERT: A 200 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: A 228 ASP cc_start: 0.8321 (m-30) cc_final: 0.7606 (t0) REVERT: A 287 ASP cc_start: 0.7537 (t0) cc_final: 0.7178 (m-30) REVERT: A 309 GLU cc_start: 0.7757 (mp0) cc_final: 0.7334 (mp0) REVERT: A 314 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 386 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7374 (mttt) REVERT: A 394 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7433 (t0) REVERT: A 424 LYS cc_start: 0.7783 (tptt) cc_final: 0.7195 (tptt) REVERT: A 465 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: A 493 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 564 GLN cc_start: 0.7331 (mm-40) cc_final: 0.7039 (mm-40) REVERT: A 578 ASP cc_start: 0.7733 (t70) cc_final: 0.7425 (t70) REVERT: A 580 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7822 (mm-40) REVERT: A 595 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 596 SER cc_start: 0.8655 (m) cc_final: 0.8241 (p) REVERT: A 610 VAL cc_start: 0.8517 (t) cc_final: 0.8252 (m) REVERT: A 642 VAL cc_start: 0.8493 (t) cc_final: 0.8159 (p) REVERT: A 651 ILE cc_start: 0.8415 (mt) cc_final: 0.8044 (mm) REVERT: A 693 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 714 ILE cc_start: 0.8096 (mm) cc_final: 0.7837 (mt) REVERT: A 733 LYS cc_start: 0.8703 (mttt) cc_final: 0.8366 (mtpp) REVERT: A 737 ASP cc_start: 0.8031 (t0) cc_final: 0.7640 (t0) REVERT: A 748 GLU cc_start: 0.7253 (tp30) cc_final: 0.6876 (tp30) REVERT: A 781 VAL cc_start: 0.8262 (p) cc_final: 0.7969 (t) REVERT: A 819 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 896 ILE cc_start: 0.8444 (mt) cc_final: 0.8191 (tt) REVERT: A 900 MET cc_start: 0.7785 (mtt) cc_final: 0.7294 (mtm) REVERT: A 904 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: A 964 LYS cc_start: 0.8685 (ttmp) cc_final: 0.8435 (ttmp) REVERT: A 983 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8381 (ttt180) REVERT: A 1019 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7370 (tpp80) REVERT: A 1029 MET cc_start: 0.8338 (tpp) cc_final: 0.7648 (tpp) REVERT: A 1096 VAL cc_start: 0.8520 (m) cc_final: 0.8214 (t) REVERT: A 1118 ASP cc_start: 0.7574 (t0) cc_final: 0.7262 (t0) REVERT: B 46 SER cc_start: 0.8514 (m) cc_final: 0.8166 (t) REVERT: B 52 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 54 LEU cc_start: 0.8663 (mp) cc_final: 0.8162 (mt) REVERT: B 61 ASN cc_start: 0.5989 (OUTLIER) cc_final: 0.5564 (p0) REVERT: B 120 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7891 (m) REVERT: B 132 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6176 (mm-30) REVERT: B 193 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.7875 (m) REVERT: B 195 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7772 (ttmm) REVERT: B 274 THR cc_start: 0.7995 (m) cc_final: 0.7596 (p) REVERT: B 279 TYR cc_start: 0.8524 (m-10) cc_final: 0.7185 (m-80) REVERT: B 289 VAL cc_start: 0.8834 (t) cc_final: 0.8493 (m) REVERT: B 599 THR cc_start: 0.8181 (m) cc_final: 0.7872 (t) REVERT: B 644 GLN cc_start: 0.8278 (tp-100) cc_final: 0.8070 (tp-100) REVERT: B 663 ASP cc_start: 0.7566 (t0) cc_final: 0.7248 (t0) REVERT: B 673 SER cc_start: 0.8604 (t) cc_final: 0.8339 (p) REVERT: B 779 GLN cc_start: 0.8204 (tp40) cc_final: 0.7990 (tp40) REVERT: B 781 VAL cc_start: 0.7868 (t) cc_final: 0.6802 (m) REVERT: B 819 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 979 ASP cc_start: 0.7639 (t0) cc_final: 0.7216 (t0) REVERT: B 1014 ARG cc_start: 0.8367 (ttm170) cc_final: 0.8120 (mtm-85) REVERT: B 1019 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7411 (ttp80) REVERT: B 1023 ASN cc_start: 0.8145 (m-40) cc_final: 0.7875 (m-40) REVERT: B 1028 LYS cc_start: 0.8130 (tppt) cc_final: 0.7782 (tttt) REVERT: B 1043 CYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6194 (m) REVERT: B 1084 ASP cc_start: 0.7379 (p0) cc_final: 0.6206 (p0) REVERT: B 1086 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7595 (mtmt) REVERT: C 46 SER cc_start: 0.8245 (m) cc_final: 0.7916 (p) REVERT: C 63 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6178 (t) REVERT: C 120 VAL cc_start: 0.8184 (t) cc_final: 0.7630 (m) REVERT: C 127 VAL cc_start: 0.8527 (t) cc_final: 0.8049 (p) REVERT: C 193 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8022 (t) REVERT: C 205 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8081 (p) REVERT: C 309 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6930 (mm-30) REVERT: C 317 ASN cc_start: 0.7756 (m-40) cc_final: 0.7154 (m-40) REVERT: C 319 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7530 (ptt-90) REVERT: C 340 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 378 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7495 (ptpt) REVERT: C 380 TYR cc_start: 0.7547 (m-10) cc_final: 0.7242 (m-10) REVERT: C 394 ASN cc_start: 0.7713 (t0) cc_final: 0.7148 (t0) REVERT: C 396 TYR cc_start: 0.8071 (m-10) cc_final: 0.7594 (m-80) REVERT: C 492 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7650 (pt) REVERT: C 535 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7995 (mtpp) REVERT: C 558 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7413 (mmtt) REVERT: C 562 PHE cc_start: 0.8188 (p90) cc_final: 0.7939 (p90) REVERT: C 581 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7601 (m) REVERT: C 619 GLU cc_start: 0.7637 (tp30) cc_final: 0.7381 (tt0) REVERT: C 671 CYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6340 (p) REVERT: C 748 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7157 (mt-10) REVERT: C 804 GLN cc_start: 0.8430 (mt0) cc_final: 0.8218 (mt0) REVERT: C 884 SER cc_start: 0.8670 (m) cc_final: 0.8396 (p) REVERT: C 887 THR cc_start: 0.8433 (m) cc_final: 0.8108 (p) REVERT: C 900 MET cc_start: 0.7946 (mtp) cc_final: 0.7554 (mtp) REVERT: C 949 GLN cc_start: 0.8106 (tp40) cc_final: 0.7796 (mm-40) REVERT: C 981 LEU cc_start: 0.8656 (mp) cc_final: 0.8010 (mp) REVERT: C 990 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 1019 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.8013 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8295 (mmmm) REVERT: C 1072 GLU cc_start: 0.8032 (pm20) cc_final: 0.7682 (pm20) REVERT: C 1086 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7955 (ttmm) REVERT: C 1111 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 1118 ASP cc_start: 0.7342 (p0) cc_final: 0.7111 (p0) outliers start: 163 outliers final: 98 residues processed: 809 average time/residue: 0.1625 time to fit residues: 207.9546 Evaluate side-chains 803 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 685 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 117 optimal weight: 0.0870 chunk 255 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 243 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 501 ASN ** C 506 GLN ** 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 = 0.4097 r_free = 0.4097 target = 0.163196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132736 restraints weight = 40565.078| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.95 r_work: 0.3528 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26387 Z= 0.163 Angle : 0.677 15.360 36005 Z= 0.334 Chirality : 0.047 0.481 4181 Planarity : 0.005 0.076 4587 Dihedral : 6.825 64.822 3532 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 6.37 % Allowed : 20.52 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3187 helix: 1.98 (0.20), residues: 681 sheet: 0.51 (0.20), residues: 662 loop : -1.15 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.021 0.001 TYR B 369 PHE 0.027 0.002 PHE B 275 TRP 0.046 0.002 TRP A 64 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (26301) covalent geometry : angle 0.65389 / 0.33 (35808) SS BOND : bond 0.00473 / 0.26 ( 37) SS BOND : angle 1.96819 / 1.28 ( 74) hydrogen bonds : bond 0.04210 / 2.76 ( 873) hydrogen bonds : angle 5.69171 / 3.91 ( 2463) Misc. bond : bond 0.00536 / 0.28 ( 8) link_BETA1-4 : bond 0.00296 / 0.22 ( 10) link_BETA1-4 : angle 1.13804 / 0.76 ( 30) link_NAG-ASN : bond 0.00523 / 0.33 ( 31) link_NAG-ASN : angle 3.06762 / 1.98 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 706 time to evaluate : 0.844 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7655 (t) cc_final: 0.6259 (p) REVERT: A 30 ASN cc_start: 0.8289 (t0) cc_final: 0.7921 (t0) REVERT: A 53 ASP cc_start: 0.7454 (t0) cc_final: 0.7059 (t0) REVERT: A 60 SER cc_start: 0.8425 (t) cc_final: 0.8169 (m) REVERT: A 200 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: A 237 ARG cc_start: 0.7017 (ptp90) cc_final: 0.6531 (ptp90) REVERT: A 281 GLU cc_start: 0.7593 (tp30) cc_final: 0.7239 (tp30) REVERT: A 287 ASP cc_start: 0.7495 (t0) cc_final: 0.7146 (m-30) REVERT: A 309 GLU cc_start: 0.7644 (mp0) cc_final: 0.7233 (mp0) REVERT: A 360 ASN cc_start: 0.7706 (m-40) cc_final: 0.7335 (m-40) REVERT: A 386 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7343 (mttt) REVERT: A 424 LYS cc_start: 0.7805 (tptt) cc_final: 0.7252 (tptt) REVERT: A 465 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: A 493 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 564 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6987 (mm-40) REVERT: A 578 ASP cc_start: 0.7757 (t70) cc_final: 0.7546 (t70) REVERT: A 595 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 596 SER cc_start: 0.8654 (m) cc_final: 0.8270 (p) REVERT: A 610 VAL cc_start: 0.8486 (t) cc_final: 0.8264 (m) REVERT: A 642 VAL cc_start: 0.8511 (t) cc_final: 0.8195 (p) REVERT: A 651 ILE cc_start: 0.8398 (mt) cc_final: 0.8077 (mm) REVERT: A 693 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 714 ILE cc_start: 0.8101 (mm) cc_final: 0.7841 (mt) REVERT: A 733 LYS cc_start: 0.8728 (mttt) cc_final: 0.8416 (mtpp) REVERT: A 737 ASP cc_start: 0.7964 (t0) cc_final: 0.7563 (t0) REVERT: A 748 GLU cc_start: 0.7175 (tp30) cc_final: 0.6842 (tp30) REVERT: A 781 VAL cc_start: 0.8353 (p) cc_final: 0.8018 (t) REVERT: A 819 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 896 ILE cc_start: 0.8394 (mt) cc_final: 0.8126 (tt) REVERT: A 900 MET cc_start: 0.7687 (mtt) cc_final: 0.7229 (mtm) REVERT: A 949 GLN cc_start: 0.8001 (tp40) cc_final: 0.7717 (tp40) REVERT: A 964 LYS cc_start: 0.8661 (ttmp) cc_final: 0.8400 (ttmp) REVERT: A 983 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8334 (ttt180) REVERT: A 1019 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7466 (tpp80) REVERT: A 1029 MET cc_start: 0.8285 (tpp) cc_final: 0.7656 (tpp) REVERT: A 1065 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 1072 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: A 1118 ASP cc_start: 0.7531 (t0) cc_final: 0.7246 (t0) REVERT: B 46 SER cc_start: 0.8604 (m) cc_final: 0.8223 (t) REVERT: B 52 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 54 LEU cc_start: 0.8670 (mp) cc_final: 0.8240 (mt) REVERT: B 132 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6299 (mm-30) REVERT: B 193 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.7843 (m) REVERT: B 195 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: B 197 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 205 SER cc_start: 0.8351 (t) cc_final: 0.8086 (p) REVERT: B 274 THR cc_start: 0.7940 (m) cc_final: 0.7679 (p) REVERT: B 279 TYR cc_start: 0.8545 (m-10) cc_final: 0.8143 (m-80) REVERT: B 289 VAL cc_start: 0.8829 (t) cc_final: 0.8547 (m) REVERT: B 578 ASP cc_start: 0.7955 (p0) cc_final: 0.7662 (p0) REVERT: B 599 THR cc_start: 0.8204 (m) cc_final: 0.7885 (t) REVERT: B 663 ASP cc_start: 0.7505 (t0) cc_final: 0.7167 (t0) REVERT: B 673 SER cc_start: 0.8605 (t) cc_final: 0.8327 (p) REVERT: B 779 GLN cc_start: 0.8203 (tp40) cc_final: 0.7991 (tp40) REVERT: B 781 VAL cc_start: 0.7965 (t) cc_final: 0.6922 (m) REVERT: B 819 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 979 ASP cc_start: 0.7549 (t0) cc_final: 0.7193 (t0) REVERT: B 985 ASP cc_start: 0.7343 (p0) cc_final: 0.7062 (p0) REVERT: B 1014 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7947 (mtm-85) REVERT: B 1019 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7327 (ttp80) REVERT: B 1023 ASN cc_start: 0.8139 (m-40) cc_final: 0.7880 (m-40) REVERT: B 1028 LYS cc_start: 0.8125 (tppt) cc_final: 0.7762 (tttt) REVERT: B 1043 CYS cc_start: 0.6465 (OUTLIER) cc_final: 0.6142 (m) REVERT: B 1086 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7607 (mtmt) REVERT: C 46 SER cc_start: 0.8211 (m) cc_final: 0.7895 (p) REVERT: C 63 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6191 (t) REVERT: C 120 VAL cc_start: 0.8211 (t) cc_final: 0.7607 (m) REVERT: C 127 VAL cc_start: 0.8498 (t) cc_final: 0.8090 (p) REVERT: C 205 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8041 (p) REVERT: C 294 ASP cc_start: 0.7360 (p0) cc_final: 0.7023 (p0) REVERT: C 309 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6832 (mm-30) REVERT: C 317 ASN cc_start: 0.7679 (m-40) cc_final: 0.7143 (m-40) REVERT: C 340 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 394 ASN cc_start: 0.7710 (t0) cc_final: 0.7101 (t0) REVERT: C 396 TYR cc_start: 0.8026 (m-10) cc_final: 0.7574 (m-80) REVERT: C 492 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (pt) REVERT: C 535 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7947 (mtpp) REVERT: C 619 GLU cc_start: 0.7550 (tp30) cc_final: 0.7293 (tt0) REVERT: C 702 GLU cc_start: 0.7561 (tt0) cc_final: 0.7308 (tt0) REVERT: C 748 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 819 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6997 (tt0) REVERT: C 884 SER cc_start: 0.8653 (m) cc_final: 0.8403 (p) REVERT: C 887 THR cc_start: 0.8444 (m) cc_final: 0.8231 (p) REVERT: C 900 MET cc_start: 0.7911 (mtp) cc_final: 0.7482 (mtp) REVERT: C 949 GLN cc_start: 0.8064 (tp40) cc_final: 0.7772 (mm-40) REVERT: C 981 LEU cc_start: 0.8630 (mp) cc_final: 0.8021 (mp) REVERT: C 1000 ARG cc_start: 0.8310 (mtt180) cc_final: 0.8093 (mtt180) REVERT: C 1019 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7974 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8241 (mmmm) REVERT: C 1072 GLU cc_start: 0.7989 (pm20) cc_final: 0.7636 (pm20) REVERT: C 1086 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7908 (ttmm) REVERT: C 1101 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.5041 (m-70) REVERT: C 1109 PHE cc_start: 0.8209 (t80) cc_final: 0.7859 (t80) REVERT: C 1111 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7357 (mt-10) outliers start: 178 outliers final: 108 residues processed: 812 average time/residue: 0.1629 time to fit residues: 209.0460 Evaluate side-chains 815 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 691 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 225 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 641 ASN A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132101 restraints weight = 40419.491| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.06 r_work: 0.3519 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26387 Z= 0.163 Angle : 0.676 14.130 36005 Z= 0.332 Chirality : 0.048 0.476 4181 Planarity : 0.005 0.079 4587 Dihedral : 6.432 67.252 3513 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 5.94 % Allowed : 21.55 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3187 helix: 1.99 (0.20), residues: 675 sheet: 0.35 (0.19), residues: 692 loop : -1.15 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.034 0.002 TYR C 904 PHE 0.026 0.002 PHE B 275 TRP 0.058 0.002 TRP A 64 HIS 0.008 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (26301) covalent geometry : angle 0.65638 / 0.33 (35808) SS BOND : bond 0.00428 / 0.22 ( 37) SS BOND : angle 1.51320 / 0.97 ( 74) hydrogen bonds : bond 0.04067 / 2.67 ( 873) hydrogen bonds : angle 5.60139 / 3.86 ( 2463) Misc. bond : bond 0.00440 / 0.23 ( 8) link_BETA1-4 : bond 0.00303 / 0.22 ( 10) link_BETA1-4 : angle 1.10393 / 0.74 ( 30) link_NAG-ASN : bond 0.00488 / 0.30 ( 31) link_NAG-ASN : angle 2.96559 / 1.92 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 692 time to evaluate : 1.017 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7529 (t) cc_final: 0.6138 (p) REVERT: A 30 ASN cc_start: 0.8247 (t0) cc_final: 0.7885 (t0) REVERT: A 53 ASP cc_start: 0.7528 (t0) cc_final: 0.7117 (t0) REVERT: A 60 SER cc_start: 0.8467 (t) cc_final: 0.8158 (m) REVERT: A 177 MET cc_start: -0.0815 (mtt) cc_final: -0.1102 (mtp) REVERT: A 200 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 237 ARG cc_start: 0.7099 (ptp90) cc_final: 0.6660 (ptp90) REVERT: A 280 ASN cc_start: 0.8344 (t0) cc_final: 0.8127 (t0) REVERT: A 281 GLU cc_start: 0.7688 (tp30) cc_final: 0.7279 (tp30) REVERT: A 287 ASP cc_start: 0.7563 (t0) cc_final: 0.7203 (m-30) REVERT: A 309 GLU cc_start: 0.7669 (mp0) cc_final: 0.7217 (mp0) REVERT: A 386 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7390 (mttt) REVERT: A 409 GLN cc_start: 0.7912 (tt0) cc_final: 0.7487 (tm-30) REVERT: A 424 LYS cc_start: 0.7840 (tptt) cc_final: 0.7267 (tptt) REVERT: A 430 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 465 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: A 493 GLN cc_start: 0.7509 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 564 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7050 (mm-40) REVERT: A 578 ASP cc_start: 0.7864 (t70) cc_final: 0.7595 (t70) REVERT: A 595 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 596 SER cc_start: 0.8680 (m) cc_final: 0.8251 (p) REVERT: A 610 VAL cc_start: 0.8509 (t) cc_final: 0.8274 (m) REVERT: A 642 VAL cc_start: 0.8562 (t) cc_final: 0.8233 (p) REVERT: A 651 ILE cc_start: 0.8382 (mt) cc_final: 0.8052 (mm) REVERT: A 693 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8530 (pt) REVERT: A 737 ASP cc_start: 0.7938 (t0) cc_final: 0.7593 (t0) REVERT: A 748 GLU cc_start: 0.7132 (tp30) cc_final: 0.6843 (tp30) REVERT: A 781 VAL cc_start: 0.8290 (p) cc_final: 0.7962 (t) REVERT: A 819 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 896 ILE cc_start: 0.8348 (mt) cc_final: 0.8081 (tt) REVERT: A 900 MET cc_start: 0.7709 (mtt) cc_final: 0.7283 (mtm) REVERT: A 964 LYS cc_start: 0.8678 (ttmp) cc_final: 0.8395 (ttmp) REVERT: A 983 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8355 (ttt180) REVERT: A 1029 MET cc_start: 0.8338 (tpp) cc_final: 0.7877 (tpp) REVERT: A 1065 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8201 (p) REVERT: A 1072 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 1118 ASP cc_start: 0.7622 (t0) cc_final: 0.7284 (t0) REVERT: B 46 SER cc_start: 0.8594 (m) cc_final: 0.8226 (t) REVERT: B 52 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 54 LEU cc_start: 0.8711 (mp) cc_final: 0.8347 (mt) REVERT: B 61 ASN cc_start: 0.6106 (OUTLIER) cc_final: 0.5826 (p0) REVERT: B 65 PHE cc_start: 0.7450 (m-10) cc_final: 0.7235 (m-10) REVERT: B 120 VAL cc_start: 0.8348 (t) cc_final: 0.7921 (m) REVERT: B 193 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.7827 (m) REVERT: B 195 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7695 (ttmm) REVERT: B 197 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 205 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8134 (p) REVERT: B 231 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 274 THR cc_start: 0.7966 (m) cc_final: 0.7693 (p) REVERT: B 279 TYR cc_start: 0.8526 (m-10) cc_final: 0.8058 (m-80) REVERT: B 289 VAL cc_start: 0.8830 (t) cc_final: 0.8537 (m) REVERT: B 532 ASN cc_start: 0.8493 (t0) cc_final: 0.8288 (t0) REVERT: B 541 PHE cc_start: 0.8419 (p90) cc_final: 0.8133 (p90) REVERT: B 568 ASP cc_start: 0.7088 (p0) cc_final: 0.6765 (p0) REVERT: B 599 THR cc_start: 0.8134 (m) cc_final: 0.7845 (t) REVERT: B 663 ASP cc_start: 0.7577 (t0) cc_final: 0.7233 (t0) REVERT: B 673 SER cc_start: 0.8586 (t) cc_final: 0.8195 (p) REVERT: B 768 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7961 (m) REVERT: B 779 GLN cc_start: 0.8223 (tp40) cc_final: 0.7992 (tp40) REVERT: B 780 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: B 781 VAL cc_start: 0.7954 (t) cc_final: 0.6891 (m) REVERT: B 819 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7069 (mt-10) REVERT: B 868 GLU cc_start: 0.7769 (tp30) cc_final: 0.7452 (tp30) REVERT: B 979 ASP cc_start: 0.7640 (t0) cc_final: 0.7265 (t0) REVERT: B 1014 ARG cc_start: 0.8336 (ttm170) cc_final: 0.7953 (mtm-85) REVERT: B 1019 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7375 (ttp80) REVERT: B 1023 ASN cc_start: 0.8137 (m-40) cc_final: 0.7864 (m-40) REVERT: B 1028 LYS cc_start: 0.8063 (tppt) cc_final: 0.7177 (tttt) REVERT: B 1086 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7676 (mtmt) REVERT: B 1127 ASP cc_start: 0.7241 (p0) cc_final: 0.7028 (p0) REVERT: C 46 SER cc_start: 0.8207 (m) cc_final: 0.7901 (p) REVERT: C 63 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6089 (t) REVERT: C 120 VAL cc_start: 0.8127 (t) cc_final: 0.7514 (m) REVERT: C 127 VAL cc_start: 0.8494 (t) cc_final: 0.8071 (p) REVERT: C 129 LYS cc_start: 0.7856 (tppt) cc_final: 0.6937 (tppt) REVERT: C 169 GLU cc_start: 0.7703 (mp0) cc_final: 0.6577 (mp0) REVERT: C 190 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7406 (mmm-85) REVERT: C 193 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7965 (t) REVERT: C 205 SER cc_start: 0.8458 (m) cc_final: 0.8023 (p) REVERT: C 294 ASP cc_start: 0.7332 (p0) cc_final: 0.7037 (p0) REVERT: C 309 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6865 (mm-30) REVERT: C 317 ASN cc_start: 0.7762 (m-40) cc_final: 0.7281 (m-40) REVERT: C 340 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 378 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7708 (ptpt) REVERT: C 394 ASN cc_start: 0.7714 (t0) cc_final: 0.6990 (t0) REVERT: C 396 TYR cc_start: 0.8015 (m-10) cc_final: 0.7543 (m-80) REVERT: C 492 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7721 (pt) REVERT: C 535 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7967 (mtpp) REVERT: C 619 GLU cc_start: 0.7582 (tp30) cc_final: 0.7289 (tt0) REVERT: C 651 ILE cc_start: 0.8530 (pt) cc_final: 0.8282 (mp) REVERT: C 671 CYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6220 (p) REVERT: C 702 GLU cc_start: 0.7683 (tt0) cc_final: 0.7462 (tt0) REVERT: C 748 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7093 (mt-10) REVERT: C 819 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7060 (tt0) REVERT: C 878 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 884 SER cc_start: 0.8641 (m) cc_final: 0.8396 (p) REVERT: C 887 THR cc_start: 0.8402 (m) cc_final: 0.8160 (p) REVERT: C 900 MET cc_start: 0.7950 (mtp) cc_final: 0.7576 (mtp) REVERT: C 949 GLN cc_start: 0.8055 (tp40) cc_final: 0.7729 (mm-40) REVERT: C 981 LEU cc_start: 0.8644 (mp) cc_final: 0.8010 (mp) REVERT: C 1010 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: C 1028 LYS cc_start: 0.7969 (mttt) cc_final: 0.7608 (mttt) REVERT: C 1045 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8261 (mmmm) REVERT: C 1072 GLU cc_start: 0.8099 (pm20) cc_final: 0.7699 (pm20) REVERT: C 1086 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7999 (ptpp) REVERT: C 1101 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.5290 (m-70) REVERT: C 1109 PHE cc_start: 0.8223 (t80) cc_final: 0.7860 (t80) REVERT: C 1111 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7374 (mt-10) outliers start: 166 outliers final: 116 residues processed: 792 average time/residue: 0.1690 time to fit residues: 211.2692 Evaluate side-chains 816 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 676 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 218 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 198 optimal weight: 0.0670 chunk 183 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 787 GLN A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131583 restraints weight = 40335.213| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.95 r_work: 0.3510 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26387 Z= 0.199 Angle : 0.686 13.767 36005 Z= 0.338 Chirality : 0.049 0.475 4181 Planarity : 0.005 0.079 4587 Dihedral : 6.464 69.969 3510 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 6.02 % Allowed : 22.16 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3187 helix: 1.94 (0.20), residues: 669 sheet: 0.29 (0.19), residues: 669 loop : -1.19 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.037 0.002 TYR A 266 PHE 0.037 0.002 PHE C 429 TRP 0.071 0.002 TRP A 64 HIS 0.010 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (26301) covalent geometry : angle 0.66616 / 0.33 (35808) SS BOND : bond 0.00503 / 0.27 ( 37) SS BOND : angle 1.57011 / 0.99 ( 74) hydrogen bonds : bond 0.04216 / 2.77 ( 873) hydrogen bonds : angle 5.60051 / 3.86 ( 2463) Misc. bond : bond 0.00507 / 0.29 ( 8) link_BETA1-4 : bond 0.00313 / 0.22 ( 10) link_BETA1-4 : angle 1.12503 / 0.75 ( 30) link_NAG-ASN : bond 0.00543 / 0.33 ( 31) link_NAG-ASN : angle 2.95331 / 1.90 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 690 time to evaluate : 0.930 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7605 (t) cc_final: 0.6173 (p) REVERT: A 30 ASN cc_start: 0.8236 (t0) cc_final: 0.7863 (t0) REVERT: A 53 ASP cc_start: 0.7514 (t0) cc_final: 0.7145 (t0) REVERT: A 60 SER cc_start: 0.8447 (t) cc_final: 0.8175 (m) REVERT: A 200 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: A 237 ARG cc_start: 0.7073 (ptp90) cc_final: 0.6643 (ptp90) REVERT: A 280 ASN cc_start: 0.8373 (t0) cc_final: 0.8151 (t0) REVERT: A 281 GLU cc_start: 0.7689 (tp30) cc_final: 0.7391 (tp30) REVERT: A 287 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: A 309 GLU cc_start: 0.7603 (mp0) cc_final: 0.7198 (mp0) REVERT: A 370 ASN cc_start: 0.6071 (t0) cc_final: 0.5594 (t0) REVERT: A 386 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7394 (mttt) REVERT: A 409 GLN cc_start: 0.7746 (tt0) cc_final: 0.6925 (tm-30) REVERT: A 424 LYS cc_start: 0.7919 (tptt) cc_final: 0.7347 (tptt) REVERT: A 430 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8120 (p) REVERT: A 465 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: A 493 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7123 (tm-30) REVERT: A 564 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7125 (mm-40) REVERT: A 595 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 596 SER cc_start: 0.8723 (m) cc_final: 0.8270 (p) REVERT: A 610 VAL cc_start: 0.8492 (t) cc_final: 0.8277 (m) REVERT: A 642 VAL cc_start: 0.8582 (t) cc_final: 0.8273 (p) REVERT: A 651 ILE cc_start: 0.8378 (mt) cc_final: 0.8079 (mm) REVERT: A 693 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (pt) REVERT: A 737 ASP cc_start: 0.7918 (t0) cc_final: 0.7603 (t0) REVERT: A 748 GLU cc_start: 0.7106 (tp30) cc_final: 0.6831 (tp30) REVERT: A 781 VAL cc_start: 0.8342 (p) cc_final: 0.8009 (t) REVERT: A 819 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 896 ILE cc_start: 0.8341 (mt) cc_final: 0.8060 (tt) REVERT: A 900 MET cc_start: 0.7715 (mtt) cc_final: 0.7300 (mtm) REVERT: A 964 LYS cc_start: 0.8645 (ttmp) cc_final: 0.8378 (ttmp) REVERT: A 983 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8463 (ttt180) REVERT: A 1029 MET cc_start: 0.8342 (tpp) cc_final: 0.7897 (tpp) REVERT: A 1065 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8297 (p) REVERT: A 1072 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: A 1118 ASP cc_start: 0.7585 (t0) cc_final: 0.7246 (t0) REVERT: B 41 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8386 (mmtm) REVERT: B 46 SER cc_start: 0.8588 (m) cc_final: 0.8246 (t) REVERT: B 52 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 54 LEU cc_start: 0.8743 (mp) cc_final: 0.8396 (mt) REVERT: B 120 VAL cc_start: 0.8416 (t) cc_final: 0.8029 (m) REVERT: B 193 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.7916 (m) REVERT: B 195 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7678 (ttmm) REVERT: B 197 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8454 (pp) REVERT: B 274 THR cc_start: 0.8019 (m) cc_final: 0.7672 (p) REVERT: B 289 VAL cc_start: 0.8830 (t) cc_final: 0.8573 (m) REVERT: B 532 ASN cc_start: 0.8496 (t0) cc_final: 0.8280 (t0) REVERT: B 541 PHE cc_start: 0.8415 (p90) cc_final: 0.8157 (p90) REVERT: B 599 THR cc_start: 0.8139 (m) cc_final: 0.7845 (t) REVERT: B 654 GLU cc_start: 0.7723 (tp30) cc_final: 0.7404 (tp30) REVERT: B 663 ASP cc_start: 0.7628 (t0) cc_final: 0.7269 (t0) REVERT: B 673 SER cc_start: 0.8596 (t) cc_final: 0.8302 (p) REVERT: B 742 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8328 (pt) REVERT: B 768 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8025 (m) REVERT: B 779 GLN cc_start: 0.8204 (tp40) cc_final: 0.7949 (tp40) REVERT: B 868 GLU cc_start: 0.7755 (tp30) cc_final: 0.7450 (tp30) REVERT: B 979 ASP cc_start: 0.7603 (t0) cc_final: 0.7223 (t0) REVERT: B 1019 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7349 (ttp80) REVERT: B 1023 ASN cc_start: 0.8119 (m-40) cc_final: 0.7868 (m-40) REVERT: B 1028 LYS cc_start: 0.8017 (tppt) cc_final: 0.7650 (tttt) REVERT: B 1082 CYS cc_start: 0.6853 (m) cc_final: 0.6642 (m) REVERT: B 1086 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7702 (mtmt) REVERT: C 46 SER cc_start: 0.8163 (m) cc_final: 0.7846 (p) REVERT: C 63 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6180 (t) REVERT: C 120 VAL cc_start: 0.8143 (t) cc_final: 0.7487 (m) REVERT: C 127 VAL cc_start: 0.8537 (t) cc_final: 0.8111 (p) REVERT: C 129 LYS cc_start: 0.7846 (tppt) cc_final: 0.7064 (tppt) REVERT: C 190 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7417 (mmm-85) REVERT: C 193 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (t) REVERT: C 205 SER cc_start: 0.8444 (m) cc_final: 0.8022 (p) REVERT: C 294 ASP cc_start: 0.7330 (p0) cc_final: 0.7017 (p0) REVERT: C 309 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 317 ASN cc_start: 0.7753 (m-40) cc_final: 0.7311 (m-40) REVERT: C 340 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 378 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7679 (ptpt) REVERT: C 394 ASN cc_start: 0.7701 (t0) cc_final: 0.6955 (t0) REVERT: C 396 TYR cc_start: 0.7974 (m-10) cc_final: 0.7525 (m-80) REVERT: C 619 GLU cc_start: 0.7571 (tp30) cc_final: 0.7320 (tt0) REVERT: C 671 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6220 (p) REVERT: C 702 GLU cc_start: 0.7660 (tt0) cc_final: 0.7456 (tt0) REVERT: C 748 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7074 (mt-10) REVERT: C 819 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7063 (tt0) REVERT: C 884 SER cc_start: 0.8660 (m) cc_final: 0.8398 (p) REVERT: C 887 THR cc_start: 0.8509 (m) cc_final: 0.8243 (p) REVERT: C 900 MET cc_start: 0.7976 (mtp) cc_final: 0.7605 (mtp) REVERT: C 935 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8327 (tp40) REVERT: C 981 LEU cc_start: 0.8644 (mp) cc_final: 0.7984 (mp) REVERT: C 1010 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: C 1045 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8279 (mmmt) REVERT: C 1072 GLU cc_start: 0.8088 (pm20) cc_final: 0.7720 (pm20) REVERT: C 1086 LYS cc_start: 0.8281 (ptpp) cc_final: 0.7984 (ptpp) REVERT: C 1101 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.5542 (m-70) REVERT: C 1109 PHE cc_start: 0.8295 (t80) cc_final: 0.7958 (t80) REVERT: C 1111 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7360 (mt-10) outliers start: 168 outliers final: 116 residues processed: 789 average time/residue: 0.1650 time to fit residues: 205.9328 Evaluate side-chains 815 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 679 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 86 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 101 optimal weight: 0.0050 chunk 316 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.4087 r_free = 0.4087 target = 0.161848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131027 restraints weight = 40428.782| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.97 r_work: 0.3530 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26387 Z= 0.152 Angle : 0.678 18.777 36005 Z= 0.333 Chirality : 0.048 0.460 4181 Planarity : 0.005 0.083 4587 Dihedral : 6.347 71.996 3509 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 5.37 % Allowed : 22.81 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3187 helix: 2.03 (0.20), residues: 663 sheet: 0.23 (0.19), residues: 685 loop : -1.16 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.037 0.001 TYR A 266 PHE 0.026 0.002 PHE A 888 TRP 0.091 0.002 TRP A 64 HIS 0.011 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (26301) covalent geometry : angle 0.66126 / 0.33 (35808) SS BOND : bond 0.00397 / 0.20 ( 37) SS BOND : angle 1.36886 / 0.86 ( 74) hydrogen bonds : bond 0.03891 / 2.56 ( 873) hydrogen bonds : angle 5.50708 / 3.80 ( 2463) Misc. bond : bond 0.00299 / 0.16 ( 8) link_BETA1-4 : bond 0.00410 / 0.29 ( 10) link_BETA1-4 : angle 1.08000 / 0.72 ( 30) link_NAG-ASN : bond 0.00499 / 0.32 ( 31) link_NAG-ASN : angle 2.78718 / 1.80 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 686 time to evaluate : 0.942 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7528 (t) cc_final: 0.6040 (p) REVERT: A 30 ASN cc_start: 0.8210 (t0) cc_final: 0.7833 (t0) REVERT: A 53 ASP cc_start: 0.7474 (t0) cc_final: 0.7144 (t0) REVERT: A 60 SER cc_start: 0.8453 (t) cc_final: 0.8182 (m) REVERT: A 200 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 280 ASN cc_start: 0.8366 (t0) cc_final: 0.8133 (t0) REVERT: A 281 GLU cc_start: 0.7647 (tp30) cc_final: 0.7372 (tp30) REVERT: A 287 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 309 GLU cc_start: 0.7563 (mp0) cc_final: 0.7155 (mp0) REVERT: A 340 GLU cc_start: 0.7533 (mp0) cc_final: 0.6917 (mp0) REVERT: A 370 ASN cc_start: 0.6092 (t0) cc_final: 0.5609 (t0) REVERT: A 386 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7371 (mttt) REVERT: A 409 GLN cc_start: 0.7654 (tt0) cc_final: 0.7394 (tt0) REVERT: A 424 LYS cc_start: 0.7870 (tptt) cc_final: 0.7320 (tptt) REVERT: A 430 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 432 CYS cc_start: 0.6889 (m) cc_final: 0.6538 (m) REVERT: A 465 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: A 493 GLN cc_start: 0.7697 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 564 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7209 (mm-40) REVERT: A 595 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8405 (p) REVERT: A 596 SER cc_start: 0.8696 (m) cc_final: 0.8239 (p) REVERT: A 610 VAL cc_start: 0.8477 (t) cc_final: 0.8261 (m) REVERT: A 642 VAL cc_start: 0.8576 (t) cc_final: 0.8273 (p) REVERT: A 651 ILE cc_start: 0.8344 (mt) cc_final: 0.8070 (mm) REVERT: A 693 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8455 (pt) REVERT: A 748 GLU cc_start: 0.7036 (tp30) cc_final: 0.6753 (tp30) REVERT: A 781 VAL cc_start: 0.8358 (p) cc_final: 0.8020 (t) REVERT: A 819 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 896 ILE cc_start: 0.8337 (mt) cc_final: 0.8052 (tt) REVERT: A 900 MET cc_start: 0.7622 (mtt) cc_final: 0.7213 (mtm) REVERT: A 964 LYS cc_start: 0.8646 (ttmp) cc_final: 0.8379 (ttmp) REVERT: A 983 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8383 (ttt180) REVERT: A 1029 MET cc_start: 0.8303 (tpp) cc_final: 0.7844 (tpp) REVERT: A 1065 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 1092 GLU cc_start: 0.7992 (pm20) cc_final: 0.7262 (pm20) REVERT: A 1106 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: A 1118 ASP cc_start: 0.7606 (t0) cc_final: 0.7201 (t0) REVERT: B 41 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8380 (mmtm) REVERT: B 46 SER cc_start: 0.8563 (m) cc_final: 0.8229 (t) REVERT: B 52 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 54 LEU cc_start: 0.8749 (mp) cc_final: 0.8415 (mt) REVERT: B 120 VAL cc_start: 0.8404 (t) cc_final: 0.8022 (m) REVERT: B 193 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.7851 (m) REVERT: B 195 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: B 197 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 205 SER cc_start: 0.8358 (t) cc_final: 0.8144 (p) REVERT: B 231 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 274 THR cc_start: 0.8018 (m) cc_final: 0.7690 (p) REVERT: B 289 VAL cc_start: 0.8804 (t) cc_final: 0.8578 (m) REVERT: B 541 PHE cc_start: 0.8387 (p90) cc_final: 0.8157 (p90) REVERT: B 568 ASP cc_start: 0.7023 (p0) cc_final: 0.6757 (p0) REVERT: B 599 THR cc_start: 0.8156 (m) cc_final: 0.7877 (t) REVERT: B 654 GLU cc_start: 0.7696 (tp30) cc_final: 0.7393 (tp30) REVERT: B 663 ASP cc_start: 0.7485 (t0) cc_final: 0.7080 (t0) REVERT: B 673 SER cc_start: 0.8583 (t) cc_final: 0.8199 (p) REVERT: B 779 GLN cc_start: 0.8174 (tp40) cc_final: 0.7951 (tp40) REVERT: B 882 ILE cc_start: 0.8245 (mm) cc_final: 0.7999 (mt) REVERT: B 979 ASP cc_start: 0.7553 (t0) cc_final: 0.7210 (t0) REVERT: B 1014 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7931 (mtm-85) REVERT: B 1019 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7325 (ttp80) REVERT: B 1023 ASN cc_start: 0.8110 (m-40) cc_final: 0.7828 (m-40) REVERT: B 1028 LYS cc_start: 0.8064 (tppt) cc_final: 0.7797 (ttmt) REVERT: B 1031 GLU cc_start: 0.7438 (tp30) cc_final: 0.6574 (mp0) REVERT: B 1086 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7753 (mtmt) REVERT: B 1132 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7535 (tt) REVERT: C 46 SER cc_start: 0.8139 (m) cc_final: 0.7826 (p) REVERT: C 63 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6157 (t) REVERT: C 129 LYS cc_start: 0.7816 (tppt) cc_final: 0.7304 (tppt) REVERT: C 190 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7373 (mmm-85) REVERT: C 193 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7883 (t) REVERT: C 205 SER cc_start: 0.8372 (m) cc_final: 0.7980 (p) REVERT: C 294 ASP cc_start: 0.7273 (p0) cc_final: 0.6954 (p0) REVERT: C 309 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 340 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 378 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7650 (ptpt) REVERT: C 394 ASN cc_start: 0.7650 (t0) cc_final: 0.6892 (t0) REVERT: C 396 TYR cc_start: 0.7935 (m-10) cc_final: 0.7536 (m-80) REVERT: C 619 GLU cc_start: 0.7540 (tp30) cc_final: 0.7255 (tt0) REVERT: C 651 ILE cc_start: 0.8482 (pt) cc_final: 0.8253 (mp) REVERT: C 671 CYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6205 (p) REVERT: C 702 GLU cc_start: 0.7616 (tt0) cc_final: 0.7400 (tt0) REVERT: C 748 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6970 (mt-10) REVERT: C 819 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7048 (tt0) REVERT: C 884 SER cc_start: 0.8654 (m) cc_final: 0.8422 (p) REVERT: C 887 THR cc_start: 0.8436 (m) cc_final: 0.8202 (p) REVERT: C 900 MET cc_start: 0.7884 (mtp) cc_final: 0.7517 (mtp) REVERT: C 949 GLN cc_start: 0.8093 (tp40) cc_final: 0.7869 (mm-40) REVERT: C 981 LEU cc_start: 0.8634 (mp) cc_final: 0.8014 (mp) REVERT: C 983 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7431 (mtp180) REVERT: C 1010 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 1045 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8216 (mmmt) REVERT: C 1072 GLU cc_start: 0.8060 (pm20) cc_final: 0.7719 (pm20) REVERT: C 1086 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7974 (ptpp) REVERT: C 1101 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.5580 (m-70) REVERT: C 1109 PHE cc_start: 0.8269 (t80) cc_final: 0.7901 (t80) REVERT: C 1111 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7322 (mt-10) REVERT: C 1118 ASP cc_start: 0.7514 (p0) cc_final: 0.7238 (p0) outliers start: 150 outliers final: 110 residues processed: 772 average time/residue: 0.1740 time to fit residues: 211.8984 Evaluate side-chains 797 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 667 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.4091 r_free = 0.4091 target = 0.162702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132181 restraints weight = 40592.312| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.96 r_work: 0.3524 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26387 Z= 0.169 Angle : 0.685 17.535 36005 Z= 0.337 Chirality : 0.048 0.458 4181 Planarity : 0.005 0.080 4587 Dihedral : 6.351 73.758 3509 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 5.26 % Allowed : 23.13 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3187 helix: 2.00 (0.20), residues: 663 sheet: 0.20 (0.19), residues: 697 loop : -1.17 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.048 0.002 TYR A 266 PHE 0.027 0.002 PHE B 562 TRP 0.109 0.003 TRP A 64 HIS 0.011 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (26301) covalent geometry : angle 0.66861 / 0.33 (35808) SS BOND : bond 0.00417 / 0.22 ( 37) SS BOND : angle 1.37152 / 0.87 ( 74) hydrogen bonds : bond 0.03948 / 2.59 ( 873) hydrogen bonds : angle 5.47816 / 3.78 ( 2463) Misc. bond : bond 0.00542 / 0.29 ( 8) link_BETA1-4 : bond 0.00292 / 0.21 ( 10) link_BETA1-4 : angle 1.07911 / 0.72 ( 30) link_NAG-ASN : bond 0.00502 / 0.32 ( 31) link_NAG-ASN : angle 2.75689 / 1.78 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 672 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7538 (t) cc_final: 0.6084 (p) REVERT: A 30 ASN cc_start: 0.8240 (t0) cc_final: 0.7846 (t0) REVERT: A 53 ASP cc_start: 0.7530 (t0) cc_final: 0.7161 (t0) REVERT: A 60 SER cc_start: 0.8473 (t) cc_final: 0.8157 (m) REVERT: A 200 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: A 280 ASN cc_start: 0.8409 (t0) cc_final: 0.8185 (t0) REVERT: A 281 GLU cc_start: 0.7729 (tp30) cc_final: 0.7447 (tp30) REVERT: A 287 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: A 309 GLU cc_start: 0.7604 (mp0) cc_final: 0.7206 (mp0) REVERT: A 340 GLU cc_start: 0.7488 (mp0) cc_final: 0.6847 (mp0) REVERT: A 370 ASN cc_start: 0.6144 (t0) cc_final: 0.5664 (t0) REVERT: A 386 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7435 (mttt) REVERT: A 409 GLN cc_start: 0.7658 (tt0) cc_final: 0.7404 (tt0) REVERT: A 424 LYS cc_start: 0.7937 (tptt) cc_final: 0.7318 (tptt) REVERT: A 430 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 465 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: A 493 GLN cc_start: 0.7710 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 564 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7228 (mm-40) REVERT: A 595 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 610 VAL cc_start: 0.8507 (t) cc_final: 0.8268 (m) REVERT: A 642 VAL cc_start: 0.8669 (t) cc_final: 0.8341 (p) REVERT: A 651 ILE cc_start: 0.8335 (mt) cc_final: 0.8095 (mm) REVERT: A 693 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8453 (pt) REVERT: A 748 GLU cc_start: 0.7079 (tp30) cc_final: 0.6734 (tp30) REVERT: A 781 VAL cc_start: 0.8291 (p) cc_final: 0.7981 (t) REVERT: A 896 ILE cc_start: 0.8343 (mt) cc_final: 0.8036 (tt) REVERT: A 900 MET cc_start: 0.7653 (mtt) cc_final: 0.7237 (mtm) REVERT: A 964 LYS cc_start: 0.8637 (ttmp) cc_final: 0.8353 (ttmp) REVERT: A 983 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8409 (ttt180) REVERT: A 1029 MET cc_start: 0.8324 (tpp) cc_final: 0.7876 (tpp) REVERT: A 1050 MET cc_start: 0.7618 (ptt) cc_final: 0.7378 (ptp) REVERT: A 1065 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 1092 GLU cc_start: 0.8006 (pm20) cc_final: 0.7739 (pm20) REVERT: A 1096 VAL cc_start: 0.8514 (m) cc_final: 0.8246 (t) REVERT: A 1106 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: A 1118 ASP cc_start: 0.7625 (t0) cc_final: 0.7263 (t0) REVERT: B 41 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8391 (mmtm) REVERT: B 46 SER cc_start: 0.8563 (m) cc_final: 0.8271 (t) REVERT: B 52 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 54 LEU cc_start: 0.8729 (mp) cc_final: 0.8383 (mt) REVERT: B 120 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.7988 (m) REVERT: B 193 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.7859 (m) REVERT: B 195 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7658 (ttmm) REVERT: B 197 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 231 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 235 ILE cc_start: 0.8504 (mp) cc_final: 0.8221 (mm) REVERT: B 274 THR cc_start: 0.8039 (m) cc_final: 0.7678 (p) REVERT: B 289 VAL cc_start: 0.8784 (t) cc_final: 0.8568 (m) REVERT: B 568 ASP cc_start: 0.7024 (p0) cc_final: 0.6714 (p0) REVERT: B 599 THR cc_start: 0.8202 (m) cc_final: 0.7909 (t) REVERT: B 654 GLU cc_start: 0.7742 (tp30) cc_final: 0.7369 (tp30) REVERT: B 673 SER cc_start: 0.8563 (t) cc_final: 0.8162 (p) REVERT: B 768 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7947 (m) REVERT: B 779 GLN cc_start: 0.8138 (tp40) cc_final: 0.7909 (tp40) REVERT: B 979 ASP cc_start: 0.7605 (t0) cc_final: 0.7252 (t0) REVERT: B 1014 ARG cc_start: 0.8349 (ttm170) cc_final: 0.8086 (mtm-85) REVERT: B 1019 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7324 (ttp80) REVERT: B 1023 ASN cc_start: 0.8117 (m-40) cc_final: 0.7828 (m-40) REVERT: B 1028 LYS cc_start: 0.8007 (tppt) cc_final: 0.7713 (ttmt) REVERT: B 1086 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7759 (mtmt) REVERT: C 46 SER cc_start: 0.8125 (m) cc_final: 0.7818 (p) REVERT: C 63 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6104 (t) REVERT: C 129 LYS cc_start: 0.7858 (tppt) cc_final: 0.7041 (tppt) REVERT: C 169 GLU cc_start: 0.8056 (mp0) cc_final: 0.7231 (mp0) REVERT: C 190 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7476 (mmm-85) REVERT: C 193 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7879 (t) REVERT: C 205 SER cc_start: 0.8376 (m) cc_final: 0.7987 (p) REVERT: C 294 ASP cc_start: 0.7271 (p0) cc_final: 0.7015 (p0) REVERT: C 309 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6854 (mm-30) REVERT: C 340 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 378 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7734 (ptpt) REVERT: C 394 ASN cc_start: 0.7619 (t0) cc_final: 0.6918 (t0) REVERT: C 396 TYR cc_start: 0.7923 (m-10) cc_final: 0.7546 (m-80) REVERT: C 619 GLU cc_start: 0.7571 (tp30) cc_final: 0.7271 (tt0) REVERT: C 651 ILE cc_start: 0.8485 (pt) cc_final: 0.8263 (mp) REVERT: C 671 CYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6278 (p) REVERT: C 675 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 692 ILE cc_start: 0.8364 (mp) cc_final: 0.8076 (mt) REVERT: C 702 GLU cc_start: 0.7762 (tt0) cc_final: 0.7544 (tt0) REVERT: C 748 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7043 (mt-10) REVERT: C 819 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7081 (tt0) REVERT: C 884 SER cc_start: 0.8609 (m) cc_final: 0.8359 (p) REVERT: C 887 THR cc_start: 0.8382 (m) cc_final: 0.8151 (p) REVERT: C 900 MET cc_start: 0.7929 (mtp) cc_final: 0.7556 (mtp) REVERT: C 949 GLN cc_start: 0.8106 (tp40) cc_final: 0.7870 (mm-40) REVERT: C 981 LEU cc_start: 0.8634 (mp) cc_final: 0.8091 (mp) REVERT: C 983 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7475 (mtp180) REVERT: C 990 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7519 (tm-30) REVERT: C 1002 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7686 (mm-40) REVERT: C 1010 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: C 1028 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7782 (mttt) REVERT: C 1045 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8241 (mmmt) REVERT: C 1086 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7992 (ptpp) REVERT: C 1101 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.5823 (m-70) REVERT: C 1109 PHE cc_start: 0.8263 (t80) cc_final: 0.7871 (t80) REVERT: C 1118 ASP cc_start: 0.7570 (p0) cc_final: 0.7303 (p0) outliers start: 147 outliers final: 108 residues processed: 758 average time/residue: 0.1681 time to fit residues: 201.6089 Evaluate side-chains 795 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 666 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 125 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 804 GLN A 969 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131454 restraints weight = 40356.274| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.94 r_work: 0.3511 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 26387 Z= 0.197 Angle : 0.703 15.918 36005 Z= 0.351 Chirality : 0.049 0.443 4181 Planarity : 0.005 0.080 4587 Dihedral : 6.379 76.324 3504 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 4.80 % Allowed : 23.81 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3187 helix: 1.85 (0.20), residues: 668 sheet: 0.13 (0.19), residues: 694 loop : -1.17 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.069 0.002 TYR A 266 PHE 0.029 0.002 PHE B 541 TRP 0.138 0.003 TRP A 64 HIS 0.013 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (26301) covalent geometry : angle 0.68683 / 0.35 (35808) SS BOND : bond 0.00491 / 0.26 ( 37) SS BOND : angle 1.53517 / 0.95 ( 74) hydrogen bonds : bond 0.04121 / 2.70 ( 873) hydrogen bonds : angle 5.52538 / 3.80 ( 2463) Misc. bond : bond 0.00932 / 0.49 ( 8) link_BETA1-4 : bond 0.00284 / 0.21 ( 10) link_BETA1-4 : angle 1.12752 / 0.76 ( 30) link_NAG-ASN : bond 0.00519 / 0.32 ( 31) link_NAG-ASN : angle 2.76607 / 1.79 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 678 time to evaluate : 0.802 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: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7613 (t) cc_final: 0.6187 (p) REVERT: A 30 ASN cc_start: 0.8249 (t0) cc_final: 0.7856 (t0) REVERT: A 53 ASP cc_start: 0.7554 (t0) cc_final: 0.7169 (t0) REVERT: A 60 SER cc_start: 0.8485 (t) cc_final: 0.8151 (m) REVERT: A 200 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: A 280 ASN cc_start: 0.8435 (t0) cc_final: 0.8208 (t0) REVERT: A 281 GLU cc_start: 0.7769 (tp30) cc_final: 0.7486 (tp30) REVERT: A 287 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: A 290 ASP cc_start: 0.7531 (t0) cc_final: 0.7209 (t0) REVERT: A 309 GLU cc_start: 0.7595 (mp0) cc_final: 0.7180 (mp0) REVERT: A 370 ASN cc_start: 0.6167 (t0) cc_final: 0.5712 (t0) REVERT: A 386 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7520 (mttt) REVERT: A 409 GLN cc_start: 0.7598 (tt0) cc_final: 0.7312 (tt0) REVERT: A 424 LYS cc_start: 0.7988 (tptt) cc_final: 0.7387 (tptt) REVERT: A 430 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 465 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 493 GLN cc_start: 0.7728 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 564 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7300 (mm-40) REVERT: A 595 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8387 (p) REVERT: A 610 VAL cc_start: 0.8525 (t) cc_final: 0.8295 (m) REVERT: A 642 VAL cc_start: 0.8652 (t) cc_final: 0.8317 (p) REVERT: A 651 ILE cc_start: 0.8358 (mt) cc_final: 0.8102 (mm) REVERT: A 693 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (pt) REVERT: A 748 GLU cc_start: 0.7094 (tp30) cc_final: 0.6746 (tp30) REVERT: A 781 VAL cc_start: 0.8292 (p) cc_final: 0.7965 (t) REVERT: A 802 PHE cc_start: 0.8431 (m-10) cc_final: 0.8223 (m-10) REVERT: A 896 ILE cc_start: 0.8343 (mt) cc_final: 0.8040 (tt) REVERT: A 900 MET cc_start: 0.7687 (mtt) cc_final: 0.7267 (mtm) REVERT: A 934 ILE cc_start: 0.8352 (tp) cc_final: 0.8056 (pt) REVERT: A 964 LYS cc_start: 0.8630 (ttmp) cc_final: 0.8353 (ttmp) REVERT: A 983 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8439 (ttt180) REVERT: A 1028 LYS cc_start: 0.8232 (mttp) cc_final: 0.8018 (mttp) REVERT: A 1029 MET cc_start: 0.8341 (tpp) cc_final: 0.7893 (tpp) REVERT: A 1065 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8261 (p) REVERT: A 1096 VAL cc_start: 0.8512 (m) cc_final: 0.8238 (t) REVERT: A 1118 ASP cc_start: 0.7618 (t0) cc_final: 0.7256 (t0) REVERT: B 46 SER cc_start: 0.8571 (m) cc_final: 0.8272 (t) REVERT: B 52 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 54 LEU cc_start: 0.8723 (mp) cc_final: 0.8377 (mt) REVERT: B 120 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 168 PHE cc_start: 0.7842 (t80) cc_final: 0.7639 (t80) REVERT: B 193 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.7825 (m) REVERT: B 195 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7638 (ttmm) REVERT: B 197 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8393 (pp) REVERT: B 231 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7705 (mp) REVERT: B 235 ILE cc_start: 0.8531 (mp) cc_final: 0.8250 (mm) REVERT: B 274 THR cc_start: 0.8073 (m) cc_final: 0.7661 (p) REVERT: B 279 TYR cc_start: 0.8453 (m-10) cc_final: 0.7768 (m-80) REVERT: B 289 VAL cc_start: 0.8788 (t) cc_final: 0.8579 (m) REVERT: B 568 ASP cc_start: 0.6982 (p0) cc_final: 0.6697 (p0) REVERT: B 577 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8018 (ttm170) REVERT: B 599 THR cc_start: 0.8239 (m) cc_final: 0.7992 (t) REVERT: B 654 GLU cc_start: 0.7727 (tp30) cc_final: 0.7375 (tp30) REVERT: B 673 SER cc_start: 0.8583 (t) cc_final: 0.8281 (p) REVERT: B 768 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 773 GLU cc_start: 0.7535 (tp30) cc_final: 0.7263 (tp30) REVERT: B 779 GLN cc_start: 0.8159 (tp40) cc_final: 0.7884 (tp40) REVERT: B 979 ASP cc_start: 0.7625 (t0) cc_final: 0.7278 (t0) REVERT: B 1019 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7435 (ttp80) REVERT: B 1023 ASN cc_start: 0.8097 (m-40) cc_final: 0.7823 (m-40) REVERT: B 1028 LYS cc_start: 0.8091 (tppt) cc_final: 0.7789 (ttmt) REVERT: B 1031 GLU cc_start: 0.7577 (tp30) cc_final: 0.6709 (mp0) REVERT: B 1086 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7733 (mtmt) REVERT: B 1132 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 46 SER cc_start: 0.8158 (m) cc_final: 0.7838 (p) REVERT: C 63 THR cc_start: 0.6641 (OUTLIER) cc_final: 0.6125 (t) REVERT: C 121 ASN cc_start: 0.7026 (t0) cc_final: 0.6628 (t0) REVERT: C 129 LYS cc_start: 0.7856 (tppt) cc_final: 0.7080 (tppt) REVERT: C 169 GLU cc_start: 0.8043 (mp0) cc_final: 0.7286 (mp0) REVERT: C 190 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7472 (mmm-85) REVERT: C 193 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7861 (t) REVERT: C 205 SER cc_start: 0.8371 (m) cc_final: 0.7990 (p) REVERT: C 294 ASP cc_start: 0.7253 (p0) cc_final: 0.7006 (p0) REVERT: C 309 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6892 (mm-30) REVERT: C 340 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 377 PHE cc_start: 0.7934 (t80) cc_final: 0.7455 (t80) REVERT: C 378 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7643 (ptpt) REVERT: C 394 ASN cc_start: 0.7641 (t0) cc_final: 0.6928 (t0) REVERT: C 396 TYR cc_start: 0.7940 (m-10) cc_final: 0.7564 (m-80) REVERT: C 457 ARG cc_start: 0.6340 (tpt90) cc_final: 0.6071 (tpt90) REVERT: C 535 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8119 (mtpp) REVERT: C 619 GLU cc_start: 0.7592 (tp30) cc_final: 0.7296 (tt0) REVERT: C 651 ILE cc_start: 0.8505 (pt) cc_final: 0.8290 (mp) REVERT: C 671 CYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6329 (p) REVERT: C 675 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7618 (tm-30) REVERT: C 692 ILE cc_start: 0.8404 (mp) cc_final: 0.8010 (mt) REVERT: C 702 GLU cc_start: 0.7763 (tt0) cc_final: 0.7558 (tt0) REVERT: C 748 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7081 (mt-10) REVERT: C 819 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7089 (tt0) REVERT: C 884 SER cc_start: 0.8617 (m) cc_final: 0.8359 (p) REVERT: C 887 THR cc_start: 0.8368 (m) cc_final: 0.8162 (p) REVERT: C 900 MET cc_start: 0.7963 (mtp) cc_final: 0.7593 (mtp) REVERT: C 949 GLN cc_start: 0.8123 (tp40) cc_final: 0.7908 (tp40) REVERT: C 981 LEU cc_start: 0.8640 (mp) cc_final: 0.8116 (mp) REVERT: C 983 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7487 (mtp180) REVERT: C 990 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7513 (tm-30) REVERT: C 1002 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7717 (mm-40) REVERT: C 1010 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: C 1028 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7753 (tttt) REVERT: C 1045 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8212 (mmmt) REVERT: C 1086 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7993 (ptpp) REVERT: C 1101 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.5985 (m-70) REVERT: C 1109 PHE cc_start: 0.8301 (t80) cc_final: 0.7905 (t80) REVERT: C 1118 ASP cc_start: 0.7606 (p0) cc_final: 0.7241 (p0) outliers start: 134 outliers final: 100 residues processed: 763 average time/residue: 0.1632 time to fit residues: 197.1272 Evaluate side-chains 788 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 667 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 101 optimal weight: 0.5980 chunk 126 optimal weight: 0.0020 chunk 295 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 271 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 969 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1119 ASN C 603 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133547 restraints weight = 40206.923| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.94 r_work: 0.3556 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26387 Z= 0.131 Angle : 0.676 14.389 36005 Z= 0.335 Chirality : 0.047 0.431 4181 Planarity : 0.005 0.084 4587 Dihedral : 6.213 78.733 3502 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 4.08 % Allowed : 24.74 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3187 helix: 2.01 (0.21), residues: 667 sheet: 0.17 (0.19), residues: 688 loop : -1.15 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.072 0.001 TYR A 266 PHE 0.026 0.002 PHE A 643 TRP 0.105 0.002 TRP A 64 HIS 0.012 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (26301) covalent geometry : angle 0.66096 / 0.33 (35808) SS BOND : bond 0.00519 / 0.26 ( 37) SS BOND : angle 1.56289 / 0.98 ( 74) hydrogen bonds : bond 0.03640 / 2.38 ( 873) hydrogen bonds : angle 5.46639 / 3.77 ( 2463) Misc. bond : bond 0.00823 / 0.43 ( 8) link_BETA1-4 : bond 0.00373 / 0.27 ( 10) link_BETA1-4 : angle 1.04889 / 0.70 ( 30) link_NAG-ASN : bond 0.00496 / 0.32 ( 31) link_NAG-ASN : angle 2.56516 / 1.67 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7130.11 seconds wall clock time: 123 minutes 4.94 seconds (7384.94 seconds total)