Starting phenix.real_space_refine on Sat Jun 21 18:44:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdg_13916/06_2025/7qdg_13916.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.017 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 112 5.16 5 C 16282 2.51 5 N 4197 2.21 5 O 4979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25570 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8356 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: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8191 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 996} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 8365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8365 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 54, 'TRANS': 1019} 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: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'NDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.26, per 1000 atoms: 0.60 Number of scatterers: 25570 At special positions: 0 Unit cell: (158.2, 159.6, 182, 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 112 16.00 O 4979 8.00 N 4197 7.00 C 16282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.98 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.00 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=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.98 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.99 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.11 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.99 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.92 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.77 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.00 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.07 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=1.94 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.98 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.97 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.98 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.98 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.82 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.71 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 Atom "HETATM24980 O5 NAG K 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NDG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " 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 B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 331 " " NAG E 1 " - " ASN A 717 " " NAG G 1 " - " ASN B 717 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 165 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN C 282 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 3.8 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5978 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 45 sheets defined 24.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.536A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.730A 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 removed outlier: 3.504A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.582A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.543A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.952A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.011A 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: 4.601A 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: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.501A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.674A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.739A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.914A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.511A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.879A 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 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.538A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.595A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.013A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.398A 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 826 removed outlier: 3.634A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.744A 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: 3.902A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.509A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.542A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.505A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.600A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.593A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.803A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.778A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.572A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.160A 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 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.660A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 4.011A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.288A 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 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.839A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.725A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.355A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.581A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.343A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.042A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.618A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.122A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.536A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.970A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.526A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 121 removed outlier: 4.352A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.696A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.676A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 3.787A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.440A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.948A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.671A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.577A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A1080 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.045A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.153A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.499A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.524A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 117 through 121 removed outlier: 3.511A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.544A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.398A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.256A 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: 3.590A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.291A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 727 removed outlier: 7.202A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.186A 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: 6.312A 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 1089 through 1090 Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.836A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.715A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.670A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.121A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.640A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 670 through 675 removed outlier: 3.701A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 727 removed outlier: 4.108A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 727 removed outlier: 4.108A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.679A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2436 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: 14.83 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 2 1.04 - 1.26: 4132 1.26 - 1.48: 10984 1.48 - 1.70: 10890 1.70 - 1.92: 142 Bond restraints: 26150 Sorted by residual: bond pdb=" C ASP C1146 " pdb=" O ASP C1146 " ideal model delta sigma weight residual 1.231 0.826 0.405 2.00e-02 2.50e+03 4.10e+02 bond pdb=" C ASP B1146 " pdb=" O ASP B1146 " ideal model delta sigma weight residual 1.231 0.966 0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" CA ASN C 165 " pdb=" C ASN C 165 " ideal model delta sigma weight residual 1.526 1.634 -0.108 1.08e-02 8.57e+03 9.97e+01 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.236 1.119 0.117 1.19e-02 7.06e+03 9.66e+01 bond pdb=" N LYS C 129 " pdb=" CA LYS C 129 " ideal model delta sigma weight residual 1.455 1.355 0.101 1.23e-02 6.61e+03 6.69e+01 ... (remaining 26145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 34936 4.46 - 8.91: 602 8.91 - 13.37: 42 13.37 - 17.82: 14 17.82 - 22.28: 5 Bond angle restraints: 35599 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.87 130.02 -10.15 1.04e+00 9.25e-01 9.53e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.18 -6.52 7.30e-01 1.88e+00 7.98e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 119.05 128.60 -9.55 1.11e+00 8.12e-01 7.41e+01 angle pdb=" CA ASP B1146 " pdb=" C ASP B1146 " pdb=" O ASP B1146 " ideal model delta sigma weight residual 120.80 106.21 14.59 1.70e+00 3.46e-01 7.36e+01 angle pdb=" N LEU B 118 " pdb=" CA LEU B 118 " pdb=" C LEU B 118 " ideal model delta sigma weight residual 108.55 122.40 -13.85 1.62e+00 3.81e-01 7.31e+01 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 15056 23.10 - 46.20: 922 46.20 - 69.30: 119 69.30 - 92.40: 51 92.40 - 115.50: 35 Dihedral angle restraints: 16183 sinusoidal: 6890 harmonic: 9293 Sorted by residual: 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 -1.31 -84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 15.56 77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -9.01 -76.99 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 16180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.661: 4166 0.661 - 1.322: 7 1.322 - 1.983: 1 1.983 - 2.644: 0 2.644 - 3.304: 1 Chirality restraints: 4175 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 0.90 -3.30 2.00e-01 2.50e+01 2.73e+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 -2.19 -0.21 2.00e-02 2.50e+03 1.11e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.77e+01 ... (remaining 4172 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.051 2.00e-02 2.50e+03 4.76e-02 2.83e+01 pdb=" C7 NAG A1309 " 0.004 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 940 " 0.026 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C SER B 940 " -0.087 2.00e-02 2.50e+03 pdb=" O SER B 940 " 0.032 2.00e-02 2.50e+03 pdb=" N THR B 941 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 940 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C SER A 940 " 0.077 2.00e-02 2.50e+03 pdb=" O SER A 940 " -0.030 2.00e-02 2.50e+03 pdb=" N THR A 941 " -0.025 2.00e-02 2.50e+03 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 24 1.99 - 2.72: 1838 2.72 - 3.45: 38033 3.45 - 4.17: 59127 4.17 - 4.90: 101447 Nonbonded interactions: 200469 Sorted by model distance: nonbonded pdb=" NH2 ARG B 34 " pdb=" OE2 GLU B 191 " model vdw 1.267 3.120 nonbonded pdb=" CZ3 TRP C 353 " pdb=" CD1 TYR C 423 " model vdw 1.273 3.640 nonbonded pdb=" CD2 PHE C 392 " pdb=" CD2 PHE C 515 " model vdw 1.421 3.640 nonbonded pdb=" CZ3 TRP C 353 " pdb=" CG TYR C 423 " model vdw 1.516 3.560 nonbonded pdb=" NZ LYS B 310 " pdb=" OD1 ASP B 663 " model vdw 1.529 3.120 ... (remaining 200464 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 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 472 or resid 49 \ 0 through 515 or resid 523 through 579 or (resid 580 and (name N or name CA or n \ ame C or name O or name CB )) or resid 581 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 (resi \ d 940 through 944 and (name N or name CA or name C or name O or name CB )) or re \ sid 945 through 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 15 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name CB or name SG )) or resid 618 throug \ h 621 or resid 641 through 827 or resid 854 through 939 or (resid 940 through 94 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 945 through \ 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 15 through 472 or resid 490 through 515 or resid 523 throu \ gh 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 1146 or resid 1301 through 1307)) } ncs_group { reference = (chain 'E' and resid 2) selection = (chain 'G' and resid 2) selection = (chain 'I' and resid 2) selection = (chain 'J' and resid 2) selection = (chain 'K' and resid 2) selection = (chain 'L' and resid 2) selection = (chain 'M' and resid 2) selection = (chain 'N' and resid 2) selection = (chain 'O' and resid 2) selection = (chain 'P' and resid 2) selection = (chain 'Q' and resid 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 65.770 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.016 0.959 26239 Z= 0.941 Angle : 1.701 42.908 35819 Z= 0.992 Chirality : 0.113 3.304 4175 Planarity : 0.007 0.060 4553 Dihedral : 15.654 115.496 10082 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 54.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.59 % Favored : 95.03 % Rotamer: Outliers : 7.17 % Allowed : 10.80 % Favored : 82.03 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3159 helix: 3.13 (0.19), residues: 640 sheet: 0.23 (0.22), residues: 594 loop : -0.90 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP A 353 HIS 0.022 0.003 HIS B1048 PHE 0.047 0.007 PHE C 565 TYR 0.055 0.006 TYR C 741 ARG 0.046 0.003 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 35) link_NAG-ASN : angle 9.06899 ( 105) link_BETA1-4 : bond 0.00859 ( 11) link_BETA1-4 : angle 2.01891 ( 33) hydrogen bonds : bond 0.27074 ( 870) hydrogen bonds : angle 9.33747 ( 2436) SS BOND : bond 0.26724 ( 41) SS BOND : angle 11.96415 ( 82) covalent geometry : bond 0.01162 (26150) covalent geometry : angle 1.52769 (35599) Misc. bond : bond 0.29046 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 665 time to evaluate : 2.589 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 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: A 53 ASP cc_start: 0.7306 (t0) cc_final: 0.6903 (t0) REVERT: A 88 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: A 141 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.5132 (tt) REVERT: A 235 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7420 (pt) REVERT: A 273 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8200 (mmm-85) REVERT: A 298 GLU cc_start: 0.8323 (tt0) cc_final: 0.7987 (tp30) REVERT: A 366 SER cc_start: 0.8730 (m) cc_final: 0.8509 (p) REVERT: A 386 LYS cc_start: 0.8994 (mttp) cc_final: 0.8763 (mtpt) REVERT: A 389 ASP cc_start: 0.6618 (m-30) cc_final: 0.6298 (m-30) REVERT: A 396 TYR cc_start: 0.7790 (m-10) cc_final: 0.7297 (m-10) REVERT: A 418 ILE cc_start: 0.8869 (tt) cc_final: 0.8645 (pt) REVERT: A 498 GLN cc_start: 0.8946 (mt0) cc_final: 0.8563 (mm-40) REVERT: A 560 LEU cc_start: 0.8431 (mp) cc_final: 0.7829 (mm) REVERT: A 563 GLN cc_start: 0.8063 (mt0) cc_final: 0.7762 (pt0) REVERT: A 611 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 641 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7040 (p0) REVERT: A 664 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 814 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8962 (mmmt) REVERT: A 820 ASP cc_start: 0.8159 (m-30) cc_final: 0.7582 (m-30) REVERT: A 824 ASN cc_start: 0.8761 (m-40) cc_final: 0.8521 (m110) REVERT: A 858 LEU cc_start: 0.7795 (mt) cc_final: 0.7458 (pt) REVERT: A 904 TYR cc_start: 0.7750 (t80) cc_final: 0.7518 (t80) REVERT: A 947 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8467 (ttpt) REVERT: A 993 ILE cc_start: 0.8695 (mt) cc_final: 0.8419 (mm) REVERT: A 997 ILE cc_start: 0.8993 (mt) cc_final: 0.8782 (mt) REVERT: A 1014 ARG cc_start: 0.7743 (mtt-85) cc_final: 0.7397 (mtp85) REVERT: A 1023 ASN cc_start: 0.7661 (m-40) cc_final: 0.7405 (m-40) REVERT: A 1041 ASP cc_start: 0.7992 (t70) cc_final: 0.7674 (t0) REVERT: A 1068 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8864 (m) REVERT: A 1139 ASP cc_start: 0.6757 (t70) cc_final: 0.6176 (t0) REVERT: B 52 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 114 THR cc_start: 0.8102 (m) cc_final: 0.7674 (p) REVERT: B 202 LYS cc_start: 0.8556 (mttt) cc_final: 0.8312 (mmmm) REVERT: B 212 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7320 (tt) REVERT: B 220 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.4855 (t80) REVERT: B 280 ASN cc_start: 0.8246 (p0) cc_final: 0.8036 (p0) REVERT: B 294 ASP cc_start: 0.8353 (m-30) cc_final: 0.7766 (m-30) REVERT: B 297 SER cc_start: 0.9039 (m) cc_final: 0.8829 (p) REVERT: B 535 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8146 (tppt) REVERT: B 557 LYS cc_start: 0.9271 (mttt) cc_final: 0.8966 (tptp) REVERT: B 558 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8737 (mmmt) REVERT: B 571 ASP cc_start: 0.8487 (m-30) cc_final: 0.7782 (t0) REVERT: B 584 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 651 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8756 (pt) REVERT: B 790 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8513 (tppt) REVERT: B 869 MET cc_start: 0.8365 (mtt) cc_final: 0.8129 (mtm) REVERT: B 947 LYS cc_start: 0.9112 (mttt) cc_final: 0.8880 (mmmm) REVERT: B 950 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7751 (p0) REVERT: B 1002 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8120 (tp-100) REVERT: B 1010 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8665 (mm-40) REVERT: B 1029 MET cc_start: 0.8661 (tpp) cc_final: 0.8445 (tpp) REVERT: B 1138 TYR cc_start: 0.7872 (m-80) cc_final: 0.7669 (m-10) REVERT: C 36 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7348 (m) REVERT: C 106 PHE cc_start: 0.7788 (m-80) cc_final: 0.6802 (m-80) REVERT: C 118 LEU cc_start: 0.8375 (tp) cc_final: 0.8074 (pp) REVERT: C 170 TYR cc_start: 0.8392 (t80) cc_final: 0.8076 (t80) REVERT: C 177 MET cc_start: 0.0480 (mtp) cc_final: -0.0094 (mtp) REVERT: C 190 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7852 (mmt180) REVERT: C 191 GLU cc_start: 0.8014 (mp0) cc_final: 0.7743 (pm20) REVERT: C 293 LEU cc_start: 0.9137 (tp) cc_final: 0.8900 (tt) REVERT: C 338 PHE cc_start: 0.7823 (m-80) cc_final: 0.7124 (m-10) REVERT: C 340 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: C 473 TYR cc_start: 0.8493 (t80) cc_final: 0.8031 (t80) REVERT: C 490 PHE cc_start: 0.8660 (t80) cc_final: 0.8350 (t80) REVERT: C 531 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 555 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8315 (t) REVERT: C 569 ILE cc_start: 0.9192 (mt) cc_final: 0.8940 (tp) REVERT: C 745 ASP cc_start: 0.8047 (m-30) cc_final: 0.7642 (t0) REVERT: C 755 GLN cc_start: 0.8348 (mt0) cc_final: 0.8041 (mt0) REVERT: C 814 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8566 (mmmt) REVERT: C 904 TYR cc_start: 0.8081 (m-80) cc_final: 0.7738 (m-10) REVERT: C 979 ASP cc_start: 0.8286 (t0) cc_final: 0.7365 (t0) REVERT: C 988 GLU cc_start: 0.8167 (tp30) cc_final: 0.7599 (tp30) REVERT: C 1040 VAL cc_start: 0.9415 (t) cc_final: 0.9118 (p) REVERT: C 1138 TYR cc_start: 0.7714 (t80) cc_final: 0.7445 (t80) outliers start: 199 outliers final: 71 residues processed: 809 average time/residue: 0.4048 time to fit residues: 498.7123 Evaluate side-chains 566 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 479 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 556 ASN 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 660 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0470 chunk 241 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 0.0970 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS A 211 ASN A 317 ASN A 321 GLN A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 658 ASN A 675 GLN A 751 ASN A 774 GLN A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 992 GLN A1023 ASN A1108 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 239 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 606 ASN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 165 ASN C 185 ASN C 207 HIS C 317 ASN C 370 ASN C 388 ASN C 487 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 751 ASN C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1083 HIS C1088 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.140713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110751 restraints weight = 60254.809| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.77 r_work: 0.3388 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26239 Z= 0.189 Angle : 0.902 17.925 35819 Z= 0.440 Chirality : 0.055 0.871 4175 Planarity : 0.005 0.050 4553 Dihedral : 11.431 98.778 4568 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 4.79 % Allowed : 15.48 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3159 helix: 2.38 (0.20), residues: 662 sheet: 0.23 (0.20), residues: 658 loop : -0.92 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 353 HIS 0.014 0.002 HIS B1088 PHE 0.035 0.003 PHE C 497 TYR 0.031 0.002 TYR A 453 ARG 0.007 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00978 ( 35) link_NAG-ASN : angle 4.81997 ( 105) link_BETA1-4 : bond 0.00585 ( 11) link_BETA1-4 : angle 1.89969 ( 33) hydrogen bonds : bond 0.05608 ( 870) hydrogen bonds : angle 6.80800 ( 2436) SS BOND : bond 0.00593 ( 41) SS BOND : angle 2.42048 ( 82) covalent geometry : bond 0.00421 (26150) covalent geometry : angle 0.85623 (35599) Misc. bond : bond 0.00777 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 530 time to evaluate : 2.777 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8855 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 83 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8224 (p) REVERT: A 104 TRP cc_start: 0.8236 (m-10) cc_final: 0.8033 (m-10) REVERT: A 191 GLU cc_start: 0.8564 (mp0) cc_final: 0.8077 (mp0) REVERT: A 202 LYS cc_start: 0.8824 (ptpt) cc_final: 0.8589 (tptt) REVERT: A 224 GLU cc_start: 0.7468 (pp20) cc_final: 0.7222 (pp20) REVERT: A 237 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8190 (ptt180) REVERT: A 273 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.7996 (mmm-85) REVERT: A 309 GLU cc_start: 0.8003 (pm20) cc_final: 0.7511 (pm20) REVERT: A 329 PHE cc_start: 0.7868 (m-10) cc_final: 0.7584 (m-10) REVERT: A 355 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8173 (mmm-85) REVERT: A 386 LYS cc_start: 0.9126 (mttp) cc_final: 0.8662 (mtmm) REVERT: A 388 ASN cc_start: 0.7989 (p0) cc_final: 0.6823 (p0) REVERT: A 389 ASP cc_start: 0.7406 (m-30) cc_final: 0.6664 (m-30) REVERT: A 396 TYR cc_start: 0.8235 (m-10) cc_final: 0.7975 (m-10) REVERT: A 453 TYR cc_start: 0.7186 (p90) cc_final: 0.6882 (p90) REVERT: A 461 LEU cc_start: 0.8248 (mt) cc_final: 0.7811 (mt) REVERT: A 529 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8218 (mmtm) REVERT: A 559 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: A 563 GLN cc_start: 0.8601 (mt0) cc_final: 0.8376 (pt0) REVERT: A 568 ASP cc_start: 0.7685 (t0) cc_final: 0.7401 (t0) REVERT: A 569 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 606 ASN cc_start: 0.9078 (m-40) cc_final: 0.8857 (m-40) REVERT: A 663 ASP cc_start: 0.8628 (t0) cc_final: 0.8244 (t0) REVERT: A 773 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8058 (mm-30) REVERT: A 779 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 787 GLN cc_start: 0.8771 (mt0) cc_final: 0.8484 (mp10) REVERT: A 790 LYS cc_start: 0.9058 (tppt) cc_final: 0.8704 (tptp) REVERT: A 814 LYS cc_start: 0.9057 (mmtm) cc_final: 0.8585 (mmmt) REVERT: A 824 ASN cc_start: 0.9001 (m-40) cc_final: 0.8707 (t0) REVERT: A 858 LEU cc_start: 0.8386 (mt) cc_final: 0.7918 (pt) REVERT: A 867 ASP cc_start: 0.8593 (p0) cc_final: 0.8303 (p0) REVERT: A 900 MET cc_start: 0.8272 (mtt) cc_final: 0.8020 (mtt) REVERT: A 904 TYR cc_start: 0.8127 (t80) cc_final: 0.7745 (t80) REVERT: A 933 LYS cc_start: 0.8539 (pptt) cc_final: 0.8259 (tppp) REVERT: A 935 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 949 GLN cc_start: 0.8948 (tt0) cc_final: 0.8434 (tp-100) REVERT: A 985 ASP cc_start: 0.8848 (t0) cc_final: 0.8221 (t70) REVERT: A 988 GLU cc_start: 0.8602 (mp0) cc_final: 0.8102 (pm20) REVERT: A 1048 HIS cc_start: 0.7899 (t-90) cc_final: 0.7692 (t-90) REVERT: A 1073 LYS cc_start: 0.9108 (tttm) cc_final: 0.8660 (ttmm) REVERT: A 1111 GLU cc_start: 0.7772 (mp0) cc_final: 0.7488 (mp0) REVERT: A 1139 ASP cc_start: 0.7106 (t70) cc_final: 0.6568 (t0) REVERT: B 53 ASP cc_start: 0.7879 (m-30) cc_final: 0.7601 (m-30) REVERT: B 104 TRP cc_start: 0.8017 (m-90) cc_final: 0.7703 (m-10) REVERT: B 106 PHE cc_start: 0.7740 (m-80) cc_final: 0.7461 (m-10) REVERT: B 191 GLU cc_start: 0.8360 (mp0) cc_final: 0.7794 (mp0) REVERT: B 212 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7502 (tp) REVERT: B 222 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.8001 (m) REVERT: B 245 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6527 (t70) REVERT: B 294 ASP cc_start: 0.8328 (m-30) cc_final: 0.8035 (m-30) REVERT: B 317 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7495 (p0) REVERT: B 535 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8479 (mmmt) REVERT: B 537 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8644 (mmtt) REVERT: B 557 LYS cc_start: 0.9251 (mttt) cc_final: 0.8966 (tptp) REVERT: B 558 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8604 (mmmm) REVERT: B 565 PHE cc_start: 0.7888 (m-10) cc_final: 0.7466 (m-10) REVERT: B 584 ILE cc_start: 0.8415 (mp) cc_final: 0.8058 (tp) REVERT: B 620 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 651 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8825 (pt) REVERT: B 654 GLU cc_start: 0.8589 (tp30) cc_final: 0.8280 (tm-30) REVERT: B 762 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 767 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (mt) REVERT: B 776 LYS cc_start: 0.9344 (tppt) cc_final: 0.8659 (tppt) REVERT: B 779 GLN cc_start: 0.9166 (tp40) cc_final: 0.8926 (mm-40) REVERT: B 780 GLU cc_start: 0.8475 (pt0) cc_final: 0.8225 (pt0) REVERT: B 790 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8209 (mtmt) REVERT: B 819 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: B 869 MET cc_start: 0.8889 (mtt) cc_final: 0.8663 (mtt) REVERT: B 947 LYS cc_start: 0.9017 (mttt) cc_final: 0.8609 (mmmm) REVERT: B 957 GLN cc_start: 0.8668 (tp40) cc_final: 0.8019 (tm-30) REVERT: B 1002 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8460 (tp-100) REVERT: B 1010 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8801 (mm-40) REVERT: B 1029 MET cc_start: 0.9035 (tpp) cc_final: 0.8746 (tpp) REVERT: B 1031 GLU cc_start: 0.8400 (tt0) cc_final: 0.8114 (tp30) REVERT: B 1123 SER cc_start: 0.8652 (t) cc_final: 0.8221 (p) REVERT: B 1138 TYR cc_start: 0.8073 (m-80) cc_final: 0.7834 (m-10) REVERT: C 43 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8838 (p90) REVERT: C 88 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7334 (p0) REVERT: C 94 SER cc_start: 0.7804 (p) cc_final: 0.7470 (t) REVERT: C 106 PHE cc_start: 0.7728 (m-80) cc_final: 0.7264 (m-80) REVERT: C 160 TYR cc_start: 0.8150 (p90) cc_final: 0.7934 (p90) REVERT: C 191 GLU cc_start: 0.8055 (mp0) cc_final: 0.7693 (pm20) REVERT: C 195 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8323 (mmtt) REVERT: C 200 TYR cc_start: 0.8203 (m-80) cc_final: 0.7941 (m-80) REVERT: C 297 SER cc_start: 0.8699 (m) cc_final: 0.8181 (p) REVERT: C 321 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8779 (mm-40) REVERT: C 357 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8174 (ttp80) REVERT: C 408 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8718 (tmm-80) REVERT: C 424 LYS cc_start: 0.7336 (ptmt) cc_final: 0.6913 (pttp) REVERT: C 506 GLN cc_start: 0.6820 (mt0) cc_final: 0.6529 (mm110) REVERT: C 513 LEU cc_start: 0.9005 (tp) cc_final: 0.8742 (mm) REVERT: C 528 LYS cc_start: 0.8983 (tptt) cc_final: 0.8771 (tptt) REVERT: C 529 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8777 (mmmt) REVERT: C 563 GLN cc_start: 0.8460 (mt0) cc_final: 0.8188 (pt0) REVERT: C 569 ILE cc_start: 0.9124 (mt) cc_final: 0.8894 (tp) REVERT: C 580 GLN cc_start: 0.7886 (tp40) cc_final: 0.7631 (tp40) REVERT: C 611 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8774 (tp) REVERT: C 661 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7025 (tm-30) REVERT: C 674 TYR cc_start: 0.7843 (t80) cc_final: 0.7415 (t80) REVERT: C 675 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8198 (pp30) REVERT: C 693 ILE cc_start: 0.9071 (pt) cc_final: 0.8670 (pt) REVERT: C 740 MET cc_start: 0.9224 (tpp) cc_final: 0.8843 (tpp) REVERT: C 745 ASP cc_start: 0.8435 (m-30) cc_final: 0.8190 (t0) REVERT: C 748 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8362 (mp0) REVERT: C 759 PHE cc_start: 0.8072 (m-80) cc_final: 0.7766 (m-80) REVERT: C 765 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8154 (ttm110) REVERT: C 776 LYS cc_start: 0.9038 (tppt) cc_final: 0.8809 (tppt) REVERT: C 780 GLU cc_start: 0.8526 (tp30) cc_final: 0.8307 (tp30) REVERT: C 796 ASP cc_start: 0.7383 (m-30) cc_final: 0.6926 (t0) REVERT: C 808 ASP cc_start: 0.8520 (p0) cc_final: 0.8298 (p0) REVERT: C 814 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8420 (mmtt) REVERT: C 819 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 886 TRP cc_start: 0.8872 (p90) cc_final: 0.8621 (p90) REVERT: C 902 MET cc_start: 0.9318 (mmm) cc_final: 0.9042 (mmm) REVERT: C 904 TYR cc_start: 0.8307 (m-80) cc_final: 0.7652 (m-10) REVERT: C 949 GLN cc_start: 0.8967 (tp40) cc_final: 0.8766 (tp-100) REVERT: C 988 GLU cc_start: 0.8470 (tp30) cc_final: 0.8196 (tt0) REVERT: C 1005 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 1073 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8818 (mmtt) REVERT: C 1092 GLU cc_start: 0.8556 (pm20) cc_final: 0.8252 (mp0) REVERT: C 1111 GLU cc_start: 0.7683 (mp0) cc_final: 0.7397 (mp0) REVERT: C 1120 THR cc_start: 0.8954 (p) cc_final: 0.8606 (t) REVERT: C 1138 TYR cc_start: 0.8112 (t80) cc_final: 0.7712 (t80) outliers start: 133 outliers final: 73 residues processed: 629 average time/residue: 0.4011 time to fit residues: 384.9973 Evaluate side-chains 543 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 455 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1023 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109995 restraints weight = 60638.798| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.68 r_work: 0.3358 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26239 Z= 0.175 Angle : 0.787 16.848 35819 Z= 0.382 Chirality : 0.049 0.566 4175 Planarity : 0.005 0.077 4553 Dihedral : 9.848 98.745 4468 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 4.14 % Allowed : 16.10 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3159 helix: 2.33 (0.20), residues: 664 sheet: 0.18 (0.19), residues: 678 loop : -0.93 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 353 HIS 0.013 0.001 HIS C1083 PHE 0.033 0.002 PHE B 823 TYR 0.025 0.002 TYR C 423 ARG 0.009 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 35) link_NAG-ASN : angle 3.95957 ( 105) link_BETA1-4 : bond 0.00453 ( 11) link_BETA1-4 : angle 1.63248 ( 33) hydrogen bonds : bond 0.04665 ( 870) hydrogen bonds : angle 6.19812 ( 2436) SS BOND : bond 0.01405 ( 41) SS BOND : angle 2.11369 ( 82) covalent geometry : bond 0.00373 (26150) covalent geometry : angle 0.75149 (35599) Misc. bond : bond 0.00339 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 482 time to evaluate : 2.657 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 revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8770 (tt0) cc_final: 0.8253 (tm-30) REVERT: A 53 ASP cc_start: 0.8320 (t0) cc_final: 0.7866 (t0) REVERT: A 55 PHE cc_start: 0.7926 (m-80) cc_final: 0.7658 (m-80) REVERT: A 84 LEU cc_start: 0.8938 (tt) cc_final: 0.8359 (tt) REVERT: A 127 VAL cc_start: 0.8523 (t) cc_final: 0.8279 (p) REVERT: A 191 GLU cc_start: 0.8630 (mp0) cc_final: 0.8344 (mp0) REVERT: A 202 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8347 (ptpt) REVERT: A 224 GLU cc_start: 0.7421 (pp20) cc_final: 0.7106 (pp20) REVERT: A 237 ARG cc_start: 0.8290 (ptp90) cc_final: 0.8028 (ttp80) REVERT: A 273 ARG cc_start: 0.8430 (mtt-85) cc_final: 0.7912 (mmm-85) REVERT: A 298 GLU cc_start: 0.8979 (tt0) cc_final: 0.8225 (tp30) REVERT: A 355 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8007 (mtp-110) REVERT: A 374 PHE cc_start: 0.7979 (m-10) cc_final: 0.7732 (m-10) REVERT: A 386 LYS cc_start: 0.9207 (mttp) cc_final: 0.8626 (mtmm) REVERT: A 388 ASN cc_start: 0.8028 (p0) cc_final: 0.7537 (p0) REVERT: A 424 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7913 (pttp) REVERT: A 461 LEU cc_start: 0.8568 (mt) cc_final: 0.8109 (mt) REVERT: A 560 LEU cc_start: 0.8904 (mm) cc_final: 0.8201 (mm) REVERT: A 563 GLN cc_start: 0.8563 (mt0) cc_final: 0.8162 (mt0) REVERT: A 569 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 597 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 725 GLU cc_start: 0.7591 (mp0) cc_final: 0.7257 (mp0) REVERT: A 740 MET cc_start: 0.8582 (tmm) cc_final: 0.7951 (tmm) REVERT: A 773 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 779 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8453 (tm-30) REVERT: A 787 GLN cc_start: 0.8827 (mt0) cc_final: 0.8409 (mp10) REVERT: A 790 LYS cc_start: 0.9058 (tppt) cc_final: 0.8756 (tptt) REVERT: A 814 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8619 (ptmm) REVERT: A 823 PHE cc_start: 0.8496 (t80) cc_final: 0.8284 (t80) REVERT: A 858 LEU cc_start: 0.8658 (mt) cc_final: 0.8101 (pt) REVERT: A 900 MET cc_start: 0.8454 (mtt) cc_final: 0.8118 (mtt) REVERT: A 904 TYR cc_start: 0.8047 (t80) cc_final: 0.7662 (t80) REVERT: A 935 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 988 GLU cc_start: 0.8582 (mp0) cc_final: 0.8295 (mp0) REVERT: A 1019 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8215 (ttp-110) REVERT: A 1041 ASP cc_start: 0.8492 (t0) cc_final: 0.8279 (t0) REVERT: A 1073 LYS cc_start: 0.9128 (tttm) cc_final: 0.8681 (ttmm) REVERT: A 1111 GLU cc_start: 0.8035 (mp0) cc_final: 0.7542 (mp0) REVERT: A 1113 GLN cc_start: 0.8421 (mp10) cc_final: 0.7944 (mp10) REVERT: A 1139 ASP cc_start: 0.7050 (t70) cc_final: 0.6636 (t0) REVERT: B 106 PHE cc_start: 0.7618 (m-80) cc_final: 0.7395 (m-10) REVERT: B 114 THR cc_start: 0.8069 (m) cc_final: 0.7693 (p) REVERT: B 191 GLU cc_start: 0.8371 (mp0) cc_final: 0.7685 (mp0) REVERT: B 222 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (m) REVERT: B 245 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6418 (t70) REVERT: B 537 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8883 (mmmt) REVERT: B 557 LYS cc_start: 0.9306 (mttt) cc_final: 0.9025 (tptp) REVERT: B 584 ILE cc_start: 0.8461 (mp) cc_final: 0.8126 (tp) REVERT: B 607 GLN cc_start: 0.8712 (tp40) cc_final: 0.8377 (tp-100) REVERT: B 654 GLU cc_start: 0.8584 (tp30) cc_final: 0.8332 (tm-30) REVERT: B 675 GLN cc_start: 0.8122 (tp40) cc_final: 0.7652 (pp30) REVERT: B 709 ASN cc_start: 0.8195 (m-40) cc_final: 0.7499 (m-40) REVERT: B 762 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 767 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8676 (mt) REVERT: B 773 GLU cc_start: 0.8816 (tp30) cc_final: 0.8449 (tp30) REVERT: B 776 LYS cc_start: 0.9338 (tppt) cc_final: 0.8496 (tppt) REVERT: B 779 GLN cc_start: 0.9128 (tp40) cc_final: 0.8902 (mm-40) REVERT: B 780 GLU cc_start: 0.8550 (pt0) cc_final: 0.8236 (pt0) REVERT: B 790 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8138 (mtmt) REVERT: B 815 ARG cc_start: 0.8227 (mtm180) cc_final: 0.8000 (mtm-85) REVERT: B 869 MET cc_start: 0.8933 (mtt) cc_final: 0.8723 (mtt) REVERT: B 872 GLN cc_start: 0.9175 (tp40) cc_final: 0.8969 (tp40) REVERT: B 933 LYS cc_start: 0.9022 (tppp) cc_final: 0.8609 (tptp) REVERT: B 947 LYS cc_start: 0.9016 (mttt) cc_final: 0.8695 (mmmm) REVERT: B 950 ASP cc_start: 0.8573 (p0) cc_final: 0.8321 (p0) REVERT: B 957 GLN cc_start: 0.8701 (tp40) cc_final: 0.8033 (tm-30) REVERT: B 981 LEU cc_start: 0.9335 (tt) cc_final: 0.9134 (tp) REVERT: B 988 GLU cc_start: 0.8411 (mp0) cc_final: 0.8187 (mp0) REVERT: B 1002 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8513 (tp-100) REVERT: B 1010 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8698 (mm-40) REVERT: B 1031 GLU cc_start: 0.8331 (tt0) cc_final: 0.8037 (tp30) REVERT: B 1123 SER cc_start: 0.8619 (t) cc_final: 0.8168 (p) REVERT: B 1138 TYR cc_start: 0.8109 (m-80) cc_final: 0.7837 (m-10) REVERT: C 88 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7612 (p0) REVERT: C 94 SER cc_start: 0.7875 (p) cc_final: 0.7459 (t) REVERT: C 160 TYR cc_start: 0.8100 (p90) cc_final: 0.7881 (p90) REVERT: C 190 ARG cc_start: 0.8868 (mtt180) cc_final: 0.8367 (mmt180) REVERT: C 191 GLU cc_start: 0.8047 (mp0) cc_final: 0.7465 (pm20) REVERT: C 194 PHE cc_start: 0.8668 (m-10) cc_final: 0.8345 (m-80) REVERT: C 195 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8178 (mmtt) REVERT: C 200 TYR cc_start: 0.8210 (m-80) cc_final: 0.7939 (m-80) REVERT: C 270 LEU cc_start: 0.8475 (mp) cc_final: 0.8264 (mp) REVERT: C 297 SER cc_start: 0.8764 (m) cc_final: 0.8241 (p) REVERT: C 298 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: C 321 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8828 (mm-40) REVERT: C 357 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8428 (ttp80) REVERT: C 408 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8627 (ttp80) REVERT: C 424 LYS cc_start: 0.7289 (ptmt) cc_final: 0.7073 (pttt) REVERT: C 457 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7621 (ttt90) REVERT: C 513 LEU cc_start: 0.8987 (tp) cc_final: 0.8753 (mm) REVERT: C 516 GLU cc_start: 0.7265 (mp0) cc_final: 0.6886 (pm20) REVERT: C 528 LYS cc_start: 0.9168 (tptt) cc_final: 0.8875 (tptt) REVERT: C 529 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8743 (mmmt) REVERT: C 563 GLN cc_start: 0.8523 (mt0) cc_final: 0.8112 (mm-40) REVERT: C 569 ILE cc_start: 0.9194 (mt) cc_final: 0.8981 (tp) REVERT: C 580 GLN cc_start: 0.7906 (tp40) cc_final: 0.7641 (tp40) REVERT: C 592 PHE cc_start: 0.6992 (m-80) cc_final: 0.6466 (m-80) REVERT: C 611 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8801 (tp) REVERT: C 655 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (p90) REVERT: C 661 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 675 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8102 (pp30) REVERT: C 693 ILE cc_start: 0.8993 (pt) cc_final: 0.8707 (pt) REVERT: C 748 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8439 (mp0) REVERT: C 755 GLN cc_start: 0.8676 (mt0) cc_final: 0.8341 (mt0) REVERT: C 765 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8304 (ttm-80) REVERT: C 773 GLU cc_start: 0.8696 (pt0) cc_final: 0.7703 (pp20) REVERT: C 776 LYS cc_start: 0.9031 (tppt) cc_final: 0.8714 (tppt) REVERT: C 779 GLN cc_start: 0.9042 (tt0) cc_final: 0.8717 (tm-30) REVERT: C 808 ASP cc_start: 0.8508 (p0) cc_final: 0.8234 (p0) REVERT: C 814 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8742 (mmmt) REVERT: C 819 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 823 PHE cc_start: 0.8267 (t80) cc_final: 0.7898 (m-80) REVERT: C 902 MET cc_start: 0.9239 (mmm) cc_final: 0.8966 (mmm) REVERT: C 904 TYR cc_start: 0.8302 (m-80) cc_final: 0.7634 (m-10) REVERT: C 1005 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 1019 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8217 (tpp80) REVERT: C 1034 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9040 (mm) REVERT: C 1041 ASP cc_start: 0.8635 (m-30) cc_final: 0.8331 (t0) REVERT: C 1073 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8832 (mmtt) REVERT: C 1111 GLU cc_start: 0.7724 (mp0) cc_final: 0.7424 (mp0) REVERT: C 1120 THR cc_start: 0.8961 (p) cc_final: 0.8645 (t) REVERT: C 1138 TYR cc_start: 0.8097 (t80) cc_final: 0.7573 (t80) outliers start: 115 outliers final: 64 residues processed: 573 average time/residue: 0.3955 time to fit residues: 345.5264 Evaluate side-chains 533 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 459 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 128 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 289 optimal weight: 0.0980 chunk 119 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 422 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1023 ASN B 66 HIS B 165 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 913 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.137884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107939 restraints weight = 60920.992| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.73 r_work: 0.3330 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26239 Z= 0.172 Angle : 0.739 15.223 35819 Z= 0.359 Chirality : 0.048 0.525 4175 Planarity : 0.004 0.073 4553 Dihedral : 8.874 96.413 4451 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 3.85 % Allowed : 17.39 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3159 helix: 2.28 (0.20), residues: 671 sheet: -0.01 (0.19), residues: 667 loop : -0.98 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 104 HIS 0.007 0.001 HIS B1083 PHE 0.030 0.002 PHE B 823 TYR 0.024 0.001 TYR C 423 ARG 0.008 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 35) link_NAG-ASN : angle 3.47955 ( 105) link_BETA1-4 : bond 0.00446 ( 11) link_BETA1-4 : angle 1.67729 ( 33) hydrogen bonds : bond 0.04215 ( 870) hydrogen bonds : angle 5.92221 ( 2436) SS BOND : bond 0.00516 ( 41) SS BOND : angle 2.14437 ( 82) covalent geometry : bond 0.00373 (26150) covalent geometry : angle 0.70709 (35599) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 476 time to evaluate : 2.507 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 revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8817 (tt0) cc_final: 0.8296 (tm-30) REVERT: A 53 ASP cc_start: 0.8339 (t0) cc_final: 0.7801 (t0) REVERT: A 55 PHE cc_start: 0.8018 (m-80) cc_final: 0.7688 (m-80) REVERT: A 84 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 104 TRP cc_start: 0.8259 (m-10) cc_final: 0.8030 (m-10) REVERT: A 191 GLU cc_start: 0.8559 (mp0) cc_final: 0.8246 (mp0) REVERT: A 202 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8229 (ptpt) REVERT: A 224 GLU cc_start: 0.7533 (pp20) cc_final: 0.7186 (pp20) REVERT: A 273 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.7841 (mmm-85) REVERT: A 298 GLU cc_start: 0.8999 (tt0) cc_final: 0.8141 (tp30) REVERT: A 309 GLU cc_start: 0.8099 (pm20) cc_final: 0.7650 (pm20) REVERT: A 319 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.7536 (ttm-80) REVERT: A 386 LYS cc_start: 0.9228 (mttp) cc_final: 0.8628 (mtmm) REVERT: A 388 ASN cc_start: 0.8287 (p0) cc_final: 0.7844 (p0) REVERT: A 424 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8140 (ptmt) REVERT: A 461 LEU cc_start: 0.8494 (mt) cc_final: 0.7995 (mt) REVERT: A 560 LEU cc_start: 0.8983 (mm) cc_final: 0.8421 (mm) REVERT: A 563 GLN cc_start: 0.8654 (mt0) cc_final: 0.8255 (mt0) REVERT: A 568 ASP cc_start: 0.7961 (t0) cc_final: 0.7758 (t0) REVERT: A 597 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8805 (p) REVERT: A 663 ASP cc_start: 0.8749 (t0) cc_final: 0.8229 (t0) REVERT: A 725 GLU cc_start: 0.7566 (mp0) cc_final: 0.7129 (mp0) REVERT: A 773 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8151 (mm-30) REVERT: A 779 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 787 GLN cc_start: 0.8839 (mt0) cc_final: 0.8393 (mp10) REVERT: A 790 LYS cc_start: 0.9043 (tppt) cc_final: 0.8750 (tptt) REVERT: A 814 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8610 (mmmt) REVERT: A 820 ASP cc_start: 0.9054 (t0) cc_final: 0.8054 (t0) REVERT: A 824 ASN cc_start: 0.9116 (t0) cc_final: 0.8800 (m110) REVERT: A 858 LEU cc_start: 0.8705 (mt) cc_final: 0.8166 (pt) REVERT: A 869 MET cc_start: 0.9088 (mtm) cc_final: 0.8766 (mtm) REVERT: A 900 MET cc_start: 0.8488 (mtt) cc_final: 0.8142 (mtt) REVERT: A 904 TYR cc_start: 0.8083 (t80) cc_final: 0.7629 (t80) REVERT: A 921 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8758 (mmmm) REVERT: A 935 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 980 ILE cc_start: 0.9278 (mm) cc_final: 0.8816 (mm) REVERT: A 988 GLU cc_start: 0.8349 (mp0) cc_final: 0.8025 (pm20) REVERT: A 1014 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8523 (ttm110) REVERT: A 1041 ASP cc_start: 0.8386 (t0) cc_final: 0.7701 (t0) REVERT: A 1073 LYS cc_start: 0.9153 (tttm) cc_final: 0.8702 (ttmm) REVERT: A 1107 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7770 (ttm170) REVERT: A 1111 GLU cc_start: 0.8054 (mp0) cc_final: 0.7356 (mp0) REVERT: A 1113 GLN cc_start: 0.8372 (mp10) cc_final: 0.7870 (mp10) REVERT: A 1139 ASP cc_start: 0.7313 (t70) cc_final: 0.6848 (t0) REVERT: B 106 PHE cc_start: 0.7615 (m-80) cc_final: 0.7380 (m-10) REVERT: B 114 THR cc_start: 0.7958 (m) cc_final: 0.7547 (p) REVERT: B 191 GLU cc_start: 0.8340 (mp0) cc_final: 0.7670 (mp0) REVERT: B 222 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8152 (m) REVERT: B 237 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.6658 (mmm-85) REVERT: B 245 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6463 (t70) REVERT: B 276 LEU cc_start: 0.8708 (tp) cc_final: 0.8387 (tp) REVERT: B 309 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 535 LYS cc_start: 0.8569 (mmmt) cc_final: 0.7754 (mmmt) REVERT: B 537 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8577 (mmtt) REVERT: B 557 LYS cc_start: 0.9312 (mttt) cc_final: 0.9004 (tptp) REVERT: B 565 PHE cc_start: 0.8007 (m-10) cc_final: 0.7749 (m-10) REVERT: B 584 ILE cc_start: 0.8249 (mp) cc_final: 0.7920 (tp) REVERT: B 675 GLN cc_start: 0.8151 (tp40) cc_final: 0.7883 (pp30) REVERT: B 762 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 765 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8618 (ttm-80) REVERT: B 767 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 773 GLU cc_start: 0.8861 (tp30) cc_final: 0.8401 (tp30) REVERT: B 776 LYS cc_start: 0.9336 (tppt) cc_final: 0.9030 (tppt) REVERT: B 780 GLU cc_start: 0.8542 (pt0) cc_final: 0.8157 (pp20) REVERT: B 790 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8420 (mtmt) REVERT: B 819 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 869 MET cc_start: 0.8966 (mtt) cc_final: 0.8753 (mtt) REVERT: B 933 LYS cc_start: 0.8978 (tppp) cc_final: 0.8544 (tptp) REVERT: B 947 LYS cc_start: 0.8916 (mttt) cc_final: 0.8671 (mmtm) REVERT: B 957 GLN cc_start: 0.8767 (tp40) cc_final: 0.8064 (tm-30) REVERT: B 988 GLU cc_start: 0.8434 (mp0) cc_final: 0.8199 (mp0) REVERT: B 1002 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8530 (tp-100) REVERT: B 1010 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8617 (mm-40) REVERT: B 1019 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8188 (mtp-110) REVERT: B 1029 MET cc_start: 0.9039 (tpp) cc_final: 0.8747 (tpp) REVERT: B 1031 GLU cc_start: 0.8361 (tt0) cc_final: 0.7953 (tp30) REVERT: B 1123 SER cc_start: 0.8615 (t) cc_final: 0.8176 (p) REVERT: B 1138 TYR cc_start: 0.8102 (m-80) cc_final: 0.7778 (m-10) REVERT: C 88 ASP cc_start: 0.8487 (m-30) cc_final: 0.7534 (p0) REVERT: C 170 TYR cc_start: 0.8232 (t80) cc_final: 0.7957 (t80) REVERT: C 190 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8337 (mmt90) REVERT: C 195 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8187 (mmtt) REVERT: C 200 TYR cc_start: 0.8257 (m-80) cc_final: 0.8001 (m-80) REVERT: C 271 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: C 297 SER cc_start: 0.8769 (m) cc_final: 0.8249 (p) REVERT: C 298 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: C 304 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8900 (mmtt) REVERT: C 314 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: C 321 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8816 (mm-40) REVERT: C 357 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8538 (ttp80) REVERT: C 378 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8116 (mmmm) REVERT: C 386 LYS cc_start: 0.9019 (mttm) cc_final: 0.8412 (mtmm) REVERT: C 402 ILE cc_start: 0.8877 (tp) cc_final: 0.8441 (mm) REVERT: C 408 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8413 (ttp80) REVERT: C 457 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7754 (ttt90) REVERT: C 516 GLU cc_start: 0.7376 (mp0) cc_final: 0.6892 (pm20) REVERT: C 528 LYS cc_start: 0.9220 (tptt) cc_final: 0.8989 (tptt) REVERT: C 529 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8926 (mmmt) REVERT: C 559 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 563 GLN cc_start: 0.8530 (mt0) cc_final: 0.8044 (mm-40) REVERT: C 580 GLN cc_start: 0.7909 (tp40) cc_final: 0.7632 (tp40) REVERT: C 606 ASN cc_start: 0.8715 (t0) cc_final: 0.8342 (t0) REVERT: C 611 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (tp) REVERT: C 655 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8172 (p90) REVERT: C 661 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7297 (tm-30) REVERT: C 675 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8176 (pp30) REVERT: C 693 ILE cc_start: 0.9096 (pt) cc_final: 0.8838 (pt) REVERT: C 725 GLU cc_start: 0.8316 (tp30) cc_final: 0.7855 (tp30) REVERT: C 748 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8488 (mp0) REVERT: C 755 GLN cc_start: 0.8668 (mt0) cc_final: 0.8341 (mt0) REVERT: C 765 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8487 (ttm-80) REVERT: C 773 GLU cc_start: 0.8697 (pt0) cc_final: 0.8027 (pp20) REVERT: C 776 LYS cc_start: 0.9079 (tppt) cc_final: 0.8740 (tppt) REVERT: C 779 GLN cc_start: 0.9046 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 808 ASP cc_start: 0.8546 (p0) cc_final: 0.8056 (p0) REVERT: C 814 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8503 (mmtt) REVERT: C 819 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 823 PHE cc_start: 0.8287 (t80) cc_final: 0.7955 (m-80) REVERT: C 902 MET cc_start: 0.9223 (mmm) cc_final: 0.8990 (mmm) REVERT: C 904 TYR cc_start: 0.8359 (m-80) cc_final: 0.7689 (m-10) REVERT: C 950 ASP cc_start: 0.8646 (t0) cc_final: 0.8313 (t0) REVERT: C 966 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9027 (mp) REVERT: C 1005 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 1034 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9129 (mm) REVERT: C 1038 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8589 (mmmt) REVERT: C 1041 ASP cc_start: 0.8504 (m-30) cc_final: 0.8284 (t0) REVERT: C 1073 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8875 (mmtt) REVERT: C 1111 GLU cc_start: 0.7741 (mp0) cc_final: 0.7466 (mp0) REVERT: C 1120 THR cc_start: 0.8993 (p) cc_final: 0.8710 (t) REVERT: C 1138 TYR cc_start: 0.8103 (t80) cc_final: 0.7592 (t80) outliers start: 107 outliers final: 69 residues processed: 555 average time/residue: 0.4063 time to fit residues: 342.6429 Evaluate side-chains 533 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 451 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 7 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 66 HIS B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 343 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100665 restraints weight = 60682.463| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.58 r_work: 0.3234 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 26239 Z= 0.376 Angle : 0.829 14.633 35819 Z= 0.416 Chirality : 0.051 0.593 4175 Planarity : 0.005 0.072 4553 Dihedral : 8.766 97.546 4445 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 4.57 % Allowed : 18.01 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3159 helix: 2.11 (0.20), residues: 657 sheet: -0.31 (0.19), residues: 683 loop : -1.20 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.008 0.001 HIS C1083 PHE 0.023 0.002 PHE C 347 TYR 0.026 0.002 TYR A 269 ARG 0.009 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 35) link_NAG-ASN : angle 3.46688 ( 105) link_BETA1-4 : bond 0.00396 ( 11) link_BETA1-4 : angle 1.77332 ( 33) hydrogen bonds : bond 0.04942 ( 870) hydrogen bonds : angle 6.13483 ( 2436) SS BOND : bond 0.00554 ( 41) SS BOND : angle 2.01388 ( 82) covalent geometry : bond 0.00760 (26150) covalent geometry : angle 0.80277 (35599) Misc. bond : bond 0.02651 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 472 time to evaluate : 2.508 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: A 52 GLN cc_start: 0.8886 (tt0) cc_final: 0.8373 (tm-30) REVERT: A 53 ASP cc_start: 0.8384 (t0) cc_final: 0.7859 (t0) REVERT: A 55 PHE cc_start: 0.8171 (m-80) cc_final: 0.7891 (m-80) REVERT: A 104 TRP cc_start: 0.8357 (m-10) cc_final: 0.8142 (m-10) REVERT: A 133 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: A 191 GLU cc_start: 0.8539 (mp0) cc_final: 0.8246 (mp0) REVERT: A 202 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8259 (ptpt) REVERT: A 224 GLU cc_start: 0.7757 (pp20) cc_final: 0.7445 (pp20) REVERT: A 235 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 273 ARG cc_start: 0.8515 (mtt-85) cc_final: 0.8263 (mtp85) REVERT: A 355 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7919 (tpp80) REVERT: A 386 LYS cc_start: 0.9250 (mttp) cc_final: 0.8808 (mtmm) REVERT: A 388 ASN cc_start: 0.8649 (p0) cc_final: 0.8279 (p0) REVERT: A 424 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8194 (ptmt) REVERT: A 461 LEU cc_start: 0.8593 (mt) cc_final: 0.8128 (mt) REVERT: A 532 ASN cc_start: 0.8822 (p0) cc_final: 0.8437 (p0) REVERT: A 560 LEU cc_start: 0.9003 (mm) cc_final: 0.8389 (mm) REVERT: A 563 GLN cc_start: 0.8675 (mt0) cc_final: 0.8254 (mt0) REVERT: A 773 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8203 (mm-30) REVERT: A 779 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8564 (tm-30) REVERT: A 787 GLN cc_start: 0.8833 (mt0) cc_final: 0.8408 (mp10) REVERT: A 790 LYS cc_start: 0.9158 (tppt) cc_final: 0.8777 (tptt) REVERT: A 814 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8735 (mmmt) REVERT: A 824 ASN cc_start: 0.9182 (t0) cc_final: 0.8975 (t0) REVERT: A 825 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9023 (mmmt) REVERT: A 858 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8565 (pt) REVERT: A 900 MET cc_start: 0.8609 (mtt) cc_final: 0.8262 (mtt) REVERT: A 904 TYR cc_start: 0.8248 (t80) cc_final: 0.7777 (t80) REVERT: A 921 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8830 (mmmm) REVERT: A 935 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 1073 LYS cc_start: 0.9239 (tttm) cc_final: 0.9005 (mmmm) REVERT: A 1111 GLU cc_start: 0.8221 (mp0) cc_final: 0.7497 (mp0) REVERT: A 1113 GLN cc_start: 0.8413 (mp10) cc_final: 0.7931 (mp10) REVERT: A 1114 ILE cc_start: 0.9251 (mp) cc_final: 0.9021 (tp) REVERT: A 1139 ASP cc_start: 0.7746 (t70) cc_final: 0.7185 (t0) REVERT: B 54 LEU cc_start: 0.8558 (mp) cc_final: 0.8296 (mp) REVERT: B 106 PHE cc_start: 0.7889 (m-80) cc_final: 0.7664 (m-80) REVERT: B 191 GLU cc_start: 0.8236 (mp0) cc_final: 0.7696 (mp0) REVERT: B 222 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8350 (m) REVERT: B 245 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6604 (t70) REVERT: B 276 LEU cc_start: 0.8800 (tp) cc_final: 0.8403 (tp) REVERT: B 319 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.7973 (ptp-110) REVERT: B 535 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8160 (mmmt) REVERT: B 537 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8614 (mmtt) REVERT: B 557 LYS cc_start: 0.9353 (mttt) cc_final: 0.9008 (tptp) REVERT: B 565 PHE cc_start: 0.8207 (m-10) cc_final: 0.7841 (m-10) REVERT: B 584 ILE cc_start: 0.8506 (mp) cc_final: 0.8152 (tp) REVERT: B 697 MET cc_start: 0.8569 (ptm) cc_final: 0.7963 (ppp) REVERT: B 740 MET cc_start: 0.8976 (tpt) cc_final: 0.8655 (tpt) REVERT: B 762 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 767 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9042 (mt) REVERT: B 773 GLU cc_start: 0.8776 (tp30) cc_final: 0.8268 (tp30) REVERT: B 776 LYS cc_start: 0.9355 (tppt) cc_final: 0.9050 (tppt) REVERT: B 780 GLU cc_start: 0.8544 (pt0) cc_final: 0.8215 (pp20) REVERT: B 790 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8562 (mtmt) REVERT: B 819 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 826 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 869 MET cc_start: 0.9065 (mtt) cc_final: 0.8642 (mtt) REVERT: B 886 TRP cc_start: 0.8795 (p90) cc_final: 0.8454 (p90) REVERT: B 933 LYS cc_start: 0.9119 (tppp) cc_final: 0.8880 (ttmm) REVERT: B 947 LYS cc_start: 0.9061 (mttt) cc_final: 0.8732 (mtmt) REVERT: B 957 GLN cc_start: 0.8884 (tp40) cc_final: 0.8031 (tm-30) REVERT: B 1002 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8517 (tm-30) REVERT: B 1010 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8776 (mm-40) REVERT: B 1019 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8500 (ttp80) REVERT: B 1029 MET cc_start: 0.8988 (tpp) cc_final: 0.8664 (tpp) REVERT: B 1038 LYS cc_start: 0.9145 (tppt) cc_final: 0.8850 (tppt) REVERT: B 1123 SER cc_start: 0.8658 (t) cc_final: 0.8310 (p) REVERT: B 1135 ASN cc_start: 0.8540 (t0) cc_final: 0.8144 (t0) REVERT: C 43 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8707 (t80) REVERT: C 88 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.7738 (p0) REVERT: C 92 PHE cc_start: 0.8329 (t80) cc_final: 0.8118 (t80) REVERT: C 141 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6579 (tt) REVERT: C 170 TYR cc_start: 0.8377 (t80) cc_final: 0.8074 (t80) REVERT: C 190 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8077 (mmt180) REVERT: C 195 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8119 (mmtt) REVERT: C 276 LEU cc_start: 0.9083 (tp) cc_final: 0.8743 (tp) REVERT: C 297 SER cc_start: 0.8915 (m) cc_final: 0.8477 (p) REVERT: C 298 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: C 304 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8939 (mmtt) REVERT: C 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: C 321 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9045 (mm-40) REVERT: C 378 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8223 (mmmm) REVERT: C 389 ASP cc_start: 0.8542 (m-30) cc_final: 0.8125 (p0) REVERT: C 408 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8419 (ttp80) REVERT: C 457 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7663 (ttt90) REVERT: C 508 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: C 529 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8977 (mmmt) REVERT: C 606 ASN cc_start: 0.8982 (t0) cc_final: 0.8721 (t0) REVERT: C 661 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7487 (tm-30) REVERT: C 740 MET cc_start: 0.8746 (tpp) cc_final: 0.8523 (tpt) REVERT: C 755 GLN cc_start: 0.8748 (mt0) cc_final: 0.8344 (mp10) REVERT: C 773 GLU cc_start: 0.8725 (pt0) cc_final: 0.8493 (pt0) REVERT: C 776 LYS cc_start: 0.9130 (tppt) cc_final: 0.8757 (tppt) REVERT: C 779 GLN cc_start: 0.9084 (tt0) cc_final: 0.8651 (tm-30) REVERT: C 808 ASP cc_start: 0.8586 (p0) cc_final: 0.8099 (p0) REVERT: C 819 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 900 MET cc_start: 0.8852 (mmm) cc_final: 0.8640 (mmt) REVERT: C 902 MET cc_start: 0.9353 (mmm) cc_final: 0.9103 (mmm) REVERT: C 904 TYR cc_start: 0.8436 (m-80) cc_final: 0.7819 (m-10) REVERT: C 1005 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 1010 GLN cc_start: 0.8997 (tp40) cc_final: 0.8011 (tp40) REVERT: C 1019 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8437 (tpp80) REVERT: C 1034 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9059 (mm) REVERT: C 1038 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8631 (mmmt) REVERT: C 1073 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8830 (mmtt) REVERT: C 1084 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8623 (m-30) REVERT: C 1120 THR cc_start: 0.9008 (p) cc_final: 0.8556 (t) REVERT: C 1138 TYR cc_start: 0.8188 (t80) cc_final: 0.7576 (t80) outliers start: 127 outliers final: 82 residues processed: 562 average time/residue: 0.3971 time to fit residues: 338.2060 Evaluate side-chains 553 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 455 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 108 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 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 = 0.3978 r_free = 0.3978 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102320 restraints weight = 60965.575| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.59 r_work: 0.3289 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 26239 Z= 0.160 Angle : 0.742 16.034 35819 Z= 0.363 Chirality : 0.047 0.374 4175 Planarity : 0.004 0.071 4553 Dihedral : 8.253 95.677 4441 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.85 % Allowed : 19.19 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3159 helix: 2.10 (0.20), residues: 670 sheet: -0.32 (0.19), residues: 669 loop : -1.15 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.004 0.001 HIS A 245 PHE 0.024 0.002 PHE A 456 TYR 0.020 0.001 TYR A1067 ARG 0.012 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 35) link_NAG-ASN : angle 3.29702 ( 105) link_BETA1-4 : bond 0.00476 ( 11) link_BETA1-4 : angle 1.45827 ( 33) hydrogen bonds : bond 0.04009 ( 870) hydrogen bonds : angle 5.84747 ( 2436) SS BOND : bond 0.00472 ( 41) SS BOND : angle 2.47524 ( 82) covalent geometry : bond 0.00350 (26150) covalent geometry : angle 0.71122 (35599) Misc. bond : bond 0.00301 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 458 time to evaluate : 2.793 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 revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8752 (tt0) cc_final: 0.8269 (tm-30) REVERT: A 53 ASP cc_start: 0.8338 (t0) cc_final: 0.7869 (t0) REVERT: A 104 TRP cc_start: 0.8284 (m-10) cc_final: 0.7979 (m-10) REVERT: A 191 GLU cc_start: 0.8475 (mp0) cc_final: 0.8170 (mp0) REVERT: A 202 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8247 (ptpt) REVERT: A 224 GLU cc_start: 0.7718 (pp20) cc_final: 0.7350 (pp20) REVERT: A 228 ASP cc_start: 0.8382 (m-30) cc_final: 0.7829 (t70) REVERT: A 235 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 237 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7489 (ttp-110) REVERT: A 273 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8230 (mmm-85) REVERT: A 298 GLU cc_start: 0.9025 (tt0) cc_final: 0.8656 (tt0) REVERT: A 386 LYS cc_start: 0.9227 (mttp) cc_final: 0.8648 (mtmm) REVERT: A 388 ASN cc_start: 0.8704 (p0) cc_final: 0.8470 (p0) REVERT: A 424 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8008 (ptmt) REVERT: A 457 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8055 (tpt-90) REVERT: A 461 LEU cc_start: 0.8569 (mt) cc_final: 0.7955 (mt) REVERT: A 560 LEU cc_start: 0.8962 (mm) cc_final: 0.8237 (mm) REVERT: A 563 GLN cc_start: 0.8620 (mt0) cc_final: 0.8072 (mt0) REVERT: A 568 ASP cc_start: 0.7614 (t0) cc_final: 0.7295 (t0) REVERT: A 569 ILE cc_start: 0.8638 (mp) cc_final: 0.8337 (tp) REVERT: A 597 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 663 ASP cc_start: 0.8760 (t0) cc_final: 0.8301 (t0) REVERT: A 697 MET cc_start: 0.8826 (tpp) cc_final: 0.8533 (tpt) REVERT: A 773 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8199 (mm-30) REVERT: A 779 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 787 GLN cc_start: 0.8754 (mt0) cc_final: 0.8339 (mp10) REVERT: A 790 LYS cc_start: 0.9167 (tppt) cc_final: 0.8758 (tptt) REVERT: A 814 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8686 (mmmt) REVERT: A 820 ASP cc_start: 0.8943 (t0) cc_final: 0.8543 (m-30) REVERT: A 824 ASN cc_start: 0.9113 (t0) cc_final: 0.8854 (t0) REVERT: A 825 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8957 (mmmt) REVERT: A 858 LEU cc_start: 0.8813 (mt) cc_final: 0.8333 (pt) REVERT: A 900 MET cc_start: 0.8608 (mtt) cc_final: 0.8220 (mtt) REVERT: A 904 TYR cc_start: 0.8166 (t80) cc_final: 0.7712 (t80) REVERT: A 921 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8680 (mmmm) REVERT: A 935 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 988 GLU cc_start: 0.8383 (mp0) cc_final: 0.8121 (pm20) REVERT: A 1073 LYS cc_start: 0.9210 (tttm) cc_final: 0.8964 (mmmm) REVERT: A 1111 GLU cc_start: 0.8195 (mp0) cc_final: 0.7543 (mp0) REVERT: A 1139 ASP cc_start: 0.7819 (t70) cc_final: 0.7242 (t0) REVERT: B 119 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9062 (mm) REVERT: B 128 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8389 (pt) REVERT: B 191 GLU cc_start: 0.8098 (mp0) cc_final: 0.7315 (pm20) REVERT: B 222 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8279 (p) REVERT: B 245 HIS cc_start: 0.7082 (OUTLIER) cc_final: 0.6611 (t70) REVERT: B 276 LEU cc_start: 0.8779 (tp) cc_final: 0.8541 (tp) REVERT: B 289 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9157 (m) REVERT: B 309 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 535 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8252 (mmmm) REVERT: B 537 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8646 (mmtt) REVERT: B 557 LYS cc_start: 0.9328 (mttt) cc_final: 0.9005 (mmtt) REVERT: B 584 ILE cc_start: 0.8261 (mp) cc_final: 0.7975 (tp) REVERT: B 654 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 697 MET cc_start: 0.8496 (ptm) cc_final: 0.7919 (ppp) REVERT: B 726 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 762 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 767 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8856 (mt) REVERT: B 773 GLU cc_start: 0.8770 (tp30) cc_final: 0.8543 (tp30) REVERT: B 776 LYS cc_start: 0.9331 (tppt) cc_final: 0.8949 (tppt) REVERT: B 780 GLU cc_start: 0.8570 (pt0) cc_final: 0.8254 (pp20) REVERT: B 790 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8496 (mtmt) REVERT: B 819 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 826 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 869 MET cc_start: 0.9037 (mtt) cc_final: 0.8761 (mtt) REVERT: B 886 TRP cc_start: 0.8732 (p90) cc_final: 0.8185 (p90) REVERT: B 933 LYS cc_start: 0.9077 (tppp) cc_final: 0.8824 (ttmm) REVERT: B 947 LYS cc_start: 0.9041 (mttt) cc_final: 0.8678 (mtmt) REVERT: B 988 GLU cc_start: 0.8509 (mp0) cc_final: 0.8305 (mp0) REVERT: B 1002 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8515 (tp-100) REVERT: B 1010 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8682 (mm-40) REVERT: B 1019 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8394 (ttp80) REVERT: B 1029 MET cc_start: 0.8991 (tpp) cc_final: 0.8636 (tpp) REVERT: B 1038 LYS cc_start: 0.9050 (tppt) cc_final: 0.8772 (tppt) REVERT: B 1041 ASP cc_start: 0.8651 (t0) cc_final: 0.8214 (t0) REVERT: B 1045 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8151 (tptt) REVERT: B 1117 THR cc_start: 0.8976 (m) cc_final: 0.8744 (p) REVERT: B 1123 SER cc_start: 0.8614 (t) cc_final: 0.8181 (p) REVERT: B 1135 ASN cc_start: 0.8504 (t0) cc_final: 0.8088 (t0) REVERT: C 43 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8772 (t80) REVERT: C 64 TRP cc_start: 0.6934 (t60) cc_final: 0.6432 (t-100) REVERT: C 88 ASP cc_start: 0.8494 (m-30) cc_final: 0.7573 (p0) REVERT: C 92 PHE cc_start: 0.8249 (t80) cc_final: 0.7752 (t80) REVERT: C 170 TYR cc_start: 0.8560 (t80) cc_final: 0.8233 (t80) REVERT: C 190 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8225 (mmt180) REVERT: C 192 PHE cc_start: 0.8131 (m-80) cc_final: 0.7898 (m-10) REVERT: C 195 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8083 (mmtt) REVERT: C 276 LEU cc_start: 0.9096 (tp) cc_final: 0.8718 (tp) REVERT: C 297 SER cc_start: 0.8739 (m) cc_final: 0.8275 (p) REVERT: C 298 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: C 304 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8906 (mmtt) REVERT: C 314 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: C 321 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8973 (mm-40) REVERT: C 378 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8187 (mmmm) REVERT: C 389 ASP cc_start: 0.8533 (m-30) cc_final: 0.8149 (p0) REVERT: C 390 LEU cc_start: 0.9078 (pp) cc_final: 0.8680 (pp) REVERT: C 408 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8604 (tmm-80) REVERT: C 437 ASN cc_start: 0.7738 (m-40) cc_final: 0.7439 (m-40) REVERT: C 457 ARG cc_start: 0.8059 (ttt90) cc_final: 0.7771 (ttt90) REVERT: C 462 LYS cc_start: 0.8564 (tptp) cc_final: 0.8270 (tptt) REVERT: C 516 GLU cc_start: 0.7291 (pm20) cc_final: 0.6932 (pm20) REVERT: C 529 LYS cc_start: 0.9268 (mmmt) cc_final: 0.8937 (mmmt) REVERT: C 558 LYS cc_start: 0.8765 (tptt) cc_final: 0.8528 (tptt) REVERT: C 559 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7732 (t80) REVERT: C 563 GLN cc_start: 0.8373 (mt0) cc_final: 0.7525 (mm-40) REVERT: C 580 GLN cc_start: 0.8275 (tp40) cc_final: 0.8067 (tp40) REVERT: C 606 ASN cc_start: 0.8897 (t0) cc_final: 0.8523 (t0) REVERT: C 661 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 755 GLN cc_start: 0.8667 (mt0) cc_final: 0.8345 (mt0) REVERT: C 761 THR cc_start: 0.9054 (m) cc_final: 0.8734 (p) REVERT: C 764 ASN cc_start: 0.9196 (m-40) cc_final: 0.8983 (m-40) REVERT: C 776 LYS cc_start: 0.9097 (tppt) cc_final: 0.8704 (tppt) REVERT: C 779 GLN cc_start: 0.8980 (tt0) cc_final: 0.8558 (tm-30) REVERT: C 808 ASP cc_start: 0.8595 (p0) cc_final: 0.8057 (p0) REVERT: C 819 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 860 VAL cc_start: 0.9526 (OUTLIER) cc_final: 0.9255 (p) REVERT: C 900 MET cc_start: 0.8654 (mmm) cc_final: 0.8419 (mmt) REVERT: C 902 MET cc_start: 0.9273 (mmm) cc_final: 0.9021 (mmm) REVERT: C 904 TYR cc_start: 0.8432 (m-80) cc_final: 0.7798 (m-10) REVERT: C 1005 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 1010 GLN cc_start: 0.8993 (tp40) cc_final: 0.8295 (tp-100) REVERT: C 1014 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8698 (tpp80) REVERT: C 1019 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8386 (tpp80) REVERT: C 1034 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9092 (mm) REVERT: C 1038 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8526 (mmmt) REVERT: C 1073 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8845 (mmtt) REVERT: C 1084 ASP cc_start: 0.8864 (m-30) cc_final: 0.8640 (m-30) REVERT: C 1111 GLU cc_start: 0.8246 (mp0) cc_final: 0.7937 (mp0) REVERT: C 1120 THR cc_start: 0.9013 (p) cc_final: 0.8570 (t) REVERT: C 1138 TYR cc_start: 0.8149 (t80) cc_final: 0.7519 (t80) REVERT: C 1139 ASP cc_start: 0.7830 (t0) cc_final: 0.7577 (t0) outliers start: 107 outliers final: 63 residues processed: 545 average time/residue: 0.4143 time to fit residues: 341.1957 Evaluate side-chains 525 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 445 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 96 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 111 optimal weight: 0.2980 chunk 149 optimal weight: 50.0000 chunk 205 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104107 restraints weight = 60923.981| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 4.61 r_work: 0.3290 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26239 Z= 0.153 Angle : 0.719 12.758 35819 Z= 0.352 Chirality : 0.046 0.362 4175 Planarity : 0.004 0.067 4553 Dihedral : 7.956 98.745 4436 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 3.53 % Allowed : 20.35 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3159 helix: 2.19 (0.20), residues: 664 sheet: -0.27 (0.19), residues: 665 loop : -1.13 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 104 HIS 0.004 0.001 HIS A 655 PHE 0.024 0.001 PHE A 55 TYR 0.019 0.001 TYR A1067 ARG 0.011 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 35) link_NAG-ASN : angle 3.11885 ( 105) link_BETA1-4 : bond 0.00405 ( 11) link_BETA1-4 : angle 1.37454 ( 33) hydrogen bonds : bond 0.03779 ( 870) hydrogen bonds : angle 5.66107 ( 2436) SS BOND : bond 0.00477 ( 41) SS BOND : angle 1.99731 ( 82) covalent geometry : bond 0.00338 (26150) covalent geometry : angle 0.69282 (35599) Misc. bond : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 456 time to evaluate : 2.700 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8666 (mtt180) REVERT: A 52 GLN cc_start: 0.8743 (tt0) cc_final: 0.8214 (tm-30) REVERT: A 53 ASP cc_start: 0.8362 (t0) cc_final: 0.8041 (t0) REVERT: A 65 PHE cc_start: 0.8079 (m-80) cc_final: 0.7820 (m-80) REVERT: A 104 TRP cc_start: 0.8343 (m-10) cc_final: 0.8019 (m-10) REVERT: A 168 PHE cc_start: 0.7436 (t80) cc_final: 0.7089 (t80) REVERT: A 191 GLU cc_start: 0.8515 (mp0) cc_final: 0.8169 (mp0) REVERT: A 202 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8187 (ptpt) REVERT: A 224 GLU cc_start: 0.7601 (pp20) cc_final: 0.7214 (pp20) REVERT: A 228 ASP cc_start: 0.8369 (m-30) cc_final: 0.7880 (t70) REVERT: A 235 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 237 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7446 (ttp-110) REVERT: A 273 ARG cc_start: 0.8425 (mtt-85) cc_final: 0.7960 (mmm-85) REVERT: A 298 GLU cc_start: 0.9076 (tt0) cc_final: 0.8667 (tt0) REVERT: A 374 PHE cc_start: 0.8001 (m-10) cc_final: 0.7739 (m-10) REVERT: A 386 LYS cc_start: 0.9227 (mttp) cc_final: 0.8698 (mtmm) REVERT: A 388 ASN cc_start: 0.8740 (p0) cc_final: 0.8465 (p0) REVERT: A 424 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8086 (ptmt) REVERT: A 461 LEU cc_start: 0.8616 (mt) cc_final: 0.8219 (mt) REVERT: A 560 LEU cc_start: 0.8974 (mm) cc_final: 0.8241 (mm) REVERT: A 563 GLN cc_start: 0.8608 (mt0) cc_final: 0.8037 (mt0) REVERT: A 568 ASP cc_start: 0.7588 (t0) cc_final: 0.7265 (t0) REVERT: A 569 ILE cc_start: 0.8650 (mp) cc_final: 0.8329 (tp) REVERT: A 663 ASP cc_start: 0.8749 (t0) cc_final: 0.8225 (t0) REVERT: A 697 MET cc_start: 0.8806 (tpp) cc_final: 0.8515 (tpt) REVERT: A 773 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8113 (mm-30) REVERT: A 779 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 787 GLN cc_start: 0.8704 (mt0) cc_final: 0.8301 (mp10) REVERT: A 790 LYS cc_start: 0.9203 (tppt) cc_final: 0.8752 (tptp) REVERT: A 814 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8667 (mmmt) REVERT: A 824 ASN cc_start: 0.9105 (t0) cc_final: 0.8862 (t0) REVERT: A 825 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8971 (mmmt) REVERT: A 858 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8379 (pt) REVERT: A 869 MET cc_start: 0.8925 (mtm) cc_final: 0.8657 (ptp) REVERT: A 900 MET cc_start: 0.8610 (mtt) cc_final: 0.8213 (mtt) REVERT: A 904 TYR cc_start: 0.8038 (t80) cc_final: 0.7599 (t80) REVERT: A 921 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8652 (mmmm) REVERT: A 935 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 988 GLU cc_start: 0.8438 (mp0) cc_final: 0.8089 (pm20) REVERT: A 1073 LYS cc_start: 0.9210 (tttm) cc_final: 0.8955 (mmmm) REVERT: A 1111 GLU cc_start: 0.8222 (mp0) cc_final: 0.7700 (mp0) REVERT: A 1139 ASP cc_start: 0.7854 (t70) cc_final: 0.7297 (t0) REVERT: B 191 GLU cc_start: 0.8085 (mp0) cc_final: 0.7675 (mp0) REVERT: B 202 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8488 (mmtm) REVERT: B 245 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6649 (t70) REVERT: B 309 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 535 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8035 (mmmm) REVERT: B 537 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8629 (mmtt) REVERT: B 557 LYS cc_start: 0.9319 (mttt) cc_final: 0.8991 (mmtt) REVERT: B 558 LYS cc_start: 0.8674 (tptp) cc_final: 0.8437 (tptp) REVERT: B 584 ILE cc_start: 0.8249 (mp) cc_final: 0.7979 (tp) REVERT: B 646 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8171 (mmp80) REVERT: B 654 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 675 GLN cc_start: 0.8096 (pp30) cc_final: 0.7874 (pp30) REVERT: B 697 MET cc_start: 0.8397 (ptm) cc_final: 0.7902 (ppp) REVERT: B 699 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 726 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 762 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 767 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8773 (mt) REVERT: B 773 GLU cc_start: 0.8671 (tp30) cc_final: 0.8296 (tp30) REVERT: B 776 LYS cc_start: 0.9327 (tppt) cc_final: 0.8966 (tppt) REVERT: B 780 GLU cc_start: 0.8561 (pt0) cc_final: 0.8251 (pp20) REVERT: B 790 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8483 (mtmt) REVERT: B 819 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 826 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 868 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8283 (pp20) REVERT: B 869 MET cc_start: 0.9027 (mtt) cc_final: 0.8588 (mtt) REVERT: B 886 TRP cc_start: 0.8757 (p90) cc_final: 0.8242 (p90) REVERT: B 900 MET cc_start: 0.8905 (mmt) cc_final: 0.8537 (mmt) REVERT: B 947 LYS cc_start: 0.9013 (mttt) cc_final: 0.8726 (mtmt) REVERT: B 1002 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8497 (tp-100) REVERT: B 1010 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8610 (mm-40) REVERT: B 1029 MET cc_start: 0.8974 (tpp) cc_final: 0.8653 (tpp) REVERT: B 1038 LYS cc_start: 0.9080 (tppt) cc_final: 0.8809 (tppt) REVERT: B 1117 THR cc_start: 0.8882 (m) cc_final: 0.8626 (p) REVERT: B 1123 SER cc_start: 0.8616 (t) cc_final: 0.8170 (p) REVERT: B 1135 ASN cc_start: 0.8553 (t0) cc_final: 0.8155 (t0) REVERT: C 43 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8774 (t80) REVERT: C 64 TRP cc_start: 0.6947 (t60) cc_final: 0.6362 (t-100) REVERT: C 88 ASP cc_start: 0.8496 (m-30) cc_final: 0.7598 (p0) REVERT: C 92 PHE cc_start: 0.8384 (t80) cc_final: 0.7893 (t80) REVERT: C 170 TYR cc_start: 0.8503 (t80) cc_final: 0.8247 (t80) REVERT: C 192 PHE cc_start: 0.8084 (m-80) cc_final: 0.7788 (m-10) REVERT: C 195 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8048 (mmtt) REVERT: C 276 LEU cc_start: 0.9062 (tp) cc_final: 0.8667 (tp) REVERT: C 297 SER cc_start: 0.8734 (m) cc_final: 0.8276 (p) REVERT: C 298 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8531 (tm-30) REVERT: C 304 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8866 (mmtt) REVERT: C 314 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: C 321 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8948 (mm-40) REVERT: C 347 PHE cc_start: 0.6798 (m-80) cc_final: 0.6264 (m-80) REVERT: C 378 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8126 (mmmm) REVERT: C 389 ASP cc_start: 0.8536 (m-30) cc_final: 0.8160 (p0) REVERT: C 390 LEU cc_start: 0.9104 (pp) cc_final: 0.8722 (pp) REVERT: C 408 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8676 (tmm-80) REVERT: C 457 ARG cc_start: 0.8007 (ttt90) cc_final: 0.7648 (ttt90) REVERT: C 490 PHE cc_start: 0.8930 (t80) cc_final: 0.8506 (t80) REVERT: C 529 LYS cc_start: 0.9222 (mmmt) cc_final: 0.9001 (mmmt) REVERT: C 558 LYS cc_start: 0.8729 (tptt) cc_final: 0.8415 (tptp) REVERT: C 559 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7659 (t80) REVERT: C 563 GLN cc_start: 0.8425 (mt0) cc_final: 0.7627 (mm-40) REVERT: C 568 ASP cc_start: 0.8183 (p0) cc_final: 0.7961 (p0) REVERT: C 580 GLN cc_start: 0.8226 (tp-100) cc_final: 0.8013 (tp40) REVERT: C 606 ASN cc_start: 0.8856 (t0) cc_final: 0.8478 (t0) REVERT: C 661 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 755 GLN cc_start: 0.8681 (mt0) cc_final: 0.8337 (mt0) REVERT: C 761 THR cc_start: 0.8924 (m) cc_final: 0.8404 (p) REVERT: C 764 ASN cc_start: 0.9223 (m-40) cc_final: 0.8958 (m-40) REVERT: C 765 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8446 (ttm-80) REVERT: C 770 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 773 GLU cc_start: 0.8782 (pt0) cc_final: 0.8125 (pp20) REVERT: C 776 LYS cc_start: 0.9091 (tppt) cc_final: 0.8695 (tppt) REVERT: C 779 GLN cc_start: 0.8926 (tt0) cc_final: 0.8517 (tm-30) REVERT: C 808 ASP cc_start: 0.8585 (p0) cc_final: 0.8056 (p0) REVERT: C 819 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 860 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9240 (p) REVERT: C 900 MET cc_start: 0.8631 (mmm) cc_final: 0.8363 (mmt) REVERT: C 902 MET cc_start: 0.9290 (mmm) cc_final: 0.9021 (mmm) REVERT: C 904 TYR cc_start: 0.8437 (m-80) cc_final: 0.7772 (m-10) REVERT: C 979 ASP cc_start: 0.8746 (t0) cc_final: 0.8397 (t0) REVERT: C 988 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8029 (mp0) REVERT: C 1005 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 1010 GLN cc_start: 0.8981 (tp40) cc_final: 0.8056 (tp-100) REVERT: C 1019 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8296 (tpp80) REVERT: C 1034 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9167 (mm) REVERT: C 1073 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8852 (mmtt) REVERT: C 1084 ASP cc_start: 0.8897 (m-30) cc_final: 0.8657 (m-30) REVERT: C 1111 GLU cc_start: 0.8254 (mp0) cc_final: 0.7958 (mp0) REVERT: C 1120 THR cc_start: 0.9003 (p) cc_final: 0.8578 (t) REVERT: C 1138 TYR cc_start: 0.8160 (t80) cc_final: 0.7493 (t80) outliers start: 98 outliers final: 60 residues processed: 529 average time/residue: 0.4010 time to fit residues: 319.9774 Evaluate side-chains 524 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 448 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 134 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 307 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 231 optimal weight: 1.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.131016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100704 restraints weight = 60819.769| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.63 r_work: 0.3290 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26239 Z= 0.162 Angle : 0.716 12.511 35819 Z= 0.355 Chirality : 0.046 0.359 4175 Planarity : 0.004 0.064 4553 Dihedral : 7.625 99.765 4428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 3.53 % Allowed : 20.81 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3159 helix: 2.25 (0.21), residues: 664 sheet: -0.23 (0.19), residues: 660 loop : -1.14 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 104 HIS 0.004 0.001 HIS A 655 PHE 0.034 0.001 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.012 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 35) link_NAG-ASN : angle 2.91867 ( 105) link_BETA1-4 : bond 0.00411 ( 11) link_BETA1-4 : angle 1.32824 ( 33) hydrogen bonds : bond 0.03699 ( 870) hydrogen bonds : angle 5.59240 ( 2436) SS BOND : bond 0.00496 ( 41) SS BOND : angle 2.16105 ( 82) covalent geometry : bond 0.00353 (26150) covalent geometry : angle 0.69153 (35599) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 461 time to evaluate : 3.675 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 revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8707 (tt0) cc_final: 0.8232 (tm-30) REVERT: A 53 ASP cc_start: 0.8315 (t0) cc_final: 0.7974 (t0) REVERT: A 55 PHE cc_start: 0.8273 (m-80) cc_final: 0.8055 (m-80) REVERT: A 65 PHE cc_start: 0.8181 (m-80) cc_final: 0.7928 (m-80) REVERT: A 104 TRP cc_start: 0.8302 (m-10) cc_final: 0.8014 (m-10) REVERT: A 191 GLU cc_start: 0.8486 (mp0) cc_final: 0.8171 (mp0) REVERT: A 202 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8192 (ptpt) REVERT: A 224 GLU cc_start: 0.7524 (pp20) cc_final: 0.7175 (pp20) REVERT: A 228 ASP cc_start: 0.8320 (m-30) cc_final: 0.7971 (t0) REVERT: A 235 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 237 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7498 (ttp-110) REVERT: A 273 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.7939 (mmm-85) REVERT: A 319 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7878 (mmm160) REVERT: A 323 THR cc_start: 0.8711 (p) cc_final: 0.8464 (p) REVERT: A 355 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: A 374 PHE cc_start: 0.7966 (m-10) cc_final: 0.7734 (m-10) REVERT: A 386 LYS cc_start: 0.9227 (mttp) cc_final: 0.8696 (mtmm) REVERT: A 388 ASN cc_start: 0.8629 (p0) cc_final: 0.8299 (p0) REVERT: A 424 LYS cc_start: 0.8531 (ptmt) cc_final: 0.8112 (ptmt) REVERT: A 457 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8117 (tpt-90) REVERT: A 461 LEU cc_start: 0.8592 (mt) cc_final: 0.8207 (mp) REVERT: A 530 SER cc_start: 0.8906 (m) cc_final: 0.8654 (t) REVERT: A 560 LEU cc_start: 0.8967 (mm) cc_final: 0.8357 (mm) REVERT: A 563 GLN cc_start: 0.8544 (mt0) cc_final: 0.8034 (mt0) REVERT: A 568 ASP cc_start: 0.7602 (t0) cc_final: 0.7240 (t0) REVERT: A 569 ILE cc_start: 0.8659 (mp) cc_final: 0.8331 (tp) REVERT: A 584 ILE cc_start: 0.8664 (mm) cc_final: 0.8029 (tp) REVERT: A 658 ASN cc_start: 0.8810 (t0) cc_final: 0.8585 (t0) REVERT: A 663 ASP cc_start: 0.8785 (t0) cc_final: 0.8240 (t0) REVERT: A 697 MET cc_start: 0.8807 (tpp) cc_final: 0.8493 (tpt) REVERT: A 773 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8118 (mm-30) REVERT: A 779 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 787 GLN cc_start: 0.8732 (mt0) cc_final: 0.8337 (mp10) REVERT: A 790 LYS cc_start: 0.9183 (tppt) cc_final: 0.8744 (tptp) REVERT: A 814 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8690 (mmmt) REVERT: A 820 ASP cc_start: 0.8978 (t0) cc_final: 0.8515 (m-30) REVERT: A 824 ASN cc_start: 0.9111 (t0) cc_final: 0.8844 (t0) REVERT: A 825 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (mmmt) REVERT: A 858 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8417 (pt) REVERT: A 868 GLU cc_start: 0.8535 (pm20) cc_final: 0.8327 (pm20) REVERT: A 869 MET cc_start: 0.8893 (mtm) cc_final: 0.8566 (ptp) REVERT: A 900 MET cc_start: 0.8599 (mtt) cc_final: 0.8182 (mtt) REVERT: A 904 TYR cc_start: 0.8037 (t80) cc_final: 0.7602 (t80) REVERT: A 921 LYS cc_start: 0.8935 (mmmt) cc_final: 0.8667 (mmmm) REVERT: A 935 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 988 GLU cc_start: 0.8403 (mp0) cc_final: 0.8088 (pm20) REVERT: A 1073 LYS cc_start: 0.9256 (tttm) cc_final: 0.9045 (mmmm) REVERT: A 1111 GLU cc_start: 0.8185 (mp0) cc_final: 0.7823 (mp0) REVERT: A 1139 ASP cc_start: 0.8116 (t70) cc_final: 0.7559 (t0) REVERT: B 191 GLU cc_start: 0.8003 (mp0) cc_final: 0.7601 (mp0) REVERT: B 222 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 245 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6697 (t70) REVERT: B 297 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 309 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 535 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8311 (mmmm) REVERT: B 537 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8611 (mmtt) REVERT: B 557 LYS cc_start: 0.9356 (mttt) cc_final: 0.9000 (mmtt) REVERT: B 584 ILE cc_start: 0.8255 (mp) cc_final: 0.7996 (tp) REVERT: B 646 ARG cc_start: 0.8521 (mmp80) cc_final: 0.8140 (mmp80) REVERT: B 675 GLN cc_start: 0.8096 (pp30) cc_final: 0.7880 (pp30) REVERT: B 697 MET cc_start: 0.8455 (ptm) cc_final: 0.7967 (ppp) REVERT: B 699 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 726 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.8919 (mp) REVERT: B 759 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7056 (t80) REVERT: B 762 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 767 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 773 GLU cc_start: 0.8712 (tp30) cc_final: 0.8332 (tp30) REVERT: B 776 LYS cc_start: 0.9322 (tppt) cc_final: 0.8970 (tppt) REVERT: B 780 GLU cc_start: 0.8582 (pt0) cc_final: 0.8293 (pp20) REVERT: B 790 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8533 (mtmt) REVERT: B 819 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 868 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8244 (pp20) REVERT: B 869 MET cc_start: 0.9023 (mtt) cc_final: 0.8672 (mtt) REVERT: B 872 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8421 (tp-100) REVERT: B 886 TRP cc_start: 0.8795 (p90) cc_final: 0.8267 (p90) REVERT: B 947 LYS cc_start: 0.9045 (mttt) cc_final: 0.8824 (mtmt) REVERT: B 1002 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8510 (tp-100) REVERT: B 1010 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8539 (mm-40) REVERT: B 1031 GLU cc_start: 0.8469 (tp30) cc_final: 0.7605 (tp30) REVERT: B 1038 LYS cc_start: 0.9061 (tppt) cc_final: 0.8837 (tppt) REVERT: B 1045 LYS cc_start: 0.8452 (tmtt) cc_final: 0.8248 (tptt) REVERT: B 1117 THR cc_start: 0.8876 (m) cc_final: 0.8618 (p) REVERT: B 1123 SER cc_start: 0.8618 (t) cc_final: 0.8179 (p) REVERT: B 1135 ASN cc_start: 0.8580 (t0) cc_final: 0.8303 (t0) REVERT: C 43 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8868 (t80) REVERT: C 64 TRP cc_start: 0.6932 (t60) cc_final: 0.6328 (t-100) REVERT: C 88 ASP cc_start: 0.8424 (m-30) cc_final: 0.7603 (p0) REVERT: C 92 PHE cc_start: 0.8331 (t80) cc_final: 0.7893 (t80) REVERT: C 170 TYR cc_start: 0.8601 (t80) cc_final: 0.8230 (t80) REVERT: C 190 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8077 (mmt180) REVERT: C 192 PHE cc_start: 0.8042 (m-80) cc_final: 0.7797 (m-10) REVERT: C 216 LEU cc_start: 0.7469 (tt) cc_final: 0.7261 (mp) REVERT: C 294 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7826 (p0) REVERT: C 297 SER cc_start: 0.8756 (m) cc_final: 0.8414 (p) REVERT: C 298 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: C 304 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8828 (mmtt) REVERT: C 314 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: C 321 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8946 (mm-40) REVERT: C 378 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8204 (mmmm) REVERT: C 389 ASP cc_start: 0.8544 (m-30) cc_final: 0.8188 (p0) REVERT: C 390 LEU cc_start: 0.9084 (pp) cc_final: 0.8730 (pp) REVERT: C 408 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8640 (tmm-80) REVERT: C 457 ARG cc_start: 0.8019 (ttt90) cc_final: 0.7668 (ttt90) REVERT: C 462 LYS cc_start: 0.8496 (tptt) cc_final: 0.8181 (tptt) REVERT: C 490 PHE cc_start: 0.8922 (t80) cc_final: 0.8494 (t80) REVERT: C 516 GLU cc_start: 0.7385 (pm20) cc_final: 0.6890 (pm20) REVERT: C 529 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8949 (mmmt) REVERT: C 558 LYS cc_start: 0.8754 (tptt) cc_final: 0.8465 (tptp) REVERT: C 559 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7678 (t80) REVERT: C 563 GLN cc_start: 0.8537 (mt0) cc_final: 0.7634 (mm-40) REVERT: C 568 ASP cc_start: 0.8188 (p0) cc_final: 0.7977 (p0) REVERT: C 571 ASP cc_start: 0.8115 (t70) cc_final: 0.7679 (t0) REVERT: C 580 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8074 (tp40) REVERT: C 606 ASN cc_start: 0.8891 (t0) cc_final: 0.8519 (t0) REVERT: C 661 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7494 (tm-30) REVERT: C 755 GLN cc_start: 0.8678 (mt0) cc_final: 0.8402 (mt0) REVERT: C 761 THR cc_start: 0.8814 (m) cc_final: 0.8454 (p) REVERT: C 773 GLU cc_start: 0.8781 (pt0) cc_final: 0.8121 (pp20) REVERT: C 776 LYS cc_start: 0.9095 (tppt) cc_final: 0.8644 (tppt) REVERT: C 779 GLN cc_start: 0.8968 (tt0) cc_final: 0.8549 (tm-30) REVERT: C 808 ASP cc_start: 0.8550 (p0) cc_final: 0.8056 (p0) REVERT: C 819 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7473 (tm-30) REVERT: C 860 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9217 (p) REVERT: C 900 MET cc_start: 0.8619 (mmm) cc_final: 0.8360 (mmt) REVERT: C 902 MET cc_start: 0.9276 (mmm) cc_final: 0.9013 (mmm) REVERT: C 904 TYR cc_start: 0.8361 (m-80) cc_final: 0.7730 (m-10) REVERT: C 933 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8625 (ttmm) REVERT: C 935 GLN cc_start: 0.8813 (pp30) cc_final: 0.8604 (tm-30) REVERT: C 979 ASP cc_start: 0.8698 (t0) cc_final: 0.8355 (t0) REVERT: C 1005 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 1010 GLN cc_start: 0.8995 (tp40) cc_final: 0.8274 (tp-100) REVERT: C 1014 ARG cc_start: 0.8901 (ttm-80) cc_final: 0.8684 (tpp80) REVERT: C 1019 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8334 (tpp80) REVERT: C 1038 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8499 (mmmm) REVERT: C 1073 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8819 (mmtt) REVERT: C 1111 GLU cc_start: 0.8314 (mp0) cc_final: 0.8008 (mp0) REVERT: C 1120 THR cc_start: 0.9001 (p) cc_final: 0.8604 (t) REVERT: C 1138 TYR cc_start: 0.8215 (t80) cc_final: 0.7520 (t80) REVERT: C 1139 ASP cc_start: 0.7893 (t0) cc_final: 0.7638 (t0) outliers start: 98 outliers final: 59 residues processed: 539 average time/residue: 0.4624 time to fit residues: 377.8444 Evaluate side-chains 512 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 437 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 104 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.132381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102731 restraints weight = 60633.067| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.59 r_work: 0.3288 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26239 Z= 0.153 Angle : 0.722 12.297 35819 Z= 0.358 Chirality : 0.046 0.355 4175 Planarity : 0.004 0.062 4553 Dihedral : 7.408 96.385 4428 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.74 % Allowed : 21.89 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3159 helix: 2.25 (0.21), residues: 667 sheet: -0.21 (0.19), residues: 654 loop : -1.15 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.008 0.001 HIS A 655 PHE 0.037 0.001 PHE B 133 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 35) link_NAG-ASN : angle 2.80662 ( 105) link_BETA1-4 : bond 0.00356 ( 11) link_BETA1-4 : angle 1.27465 ( 33) hydrogen bonds : bond 0.03591 ( 870) hydrogen bonds : angle 5.49110 ( 2436) SS BOND : bond 0.00472 ( 41) SS BOND : angle 2.22589 ( 82) covalent geometry : bond 0.00339 (26150) covalent geometry : angle 0.69897 (35599) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 450 time to evaluate : 4.188 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 REVERT: A 52 GLN cc_start: 0.8761 (tt0) cc_final: 0.8273 (tm-30) REVERT: A 53 ASP cc_start: 0.8326 (t0) cc_final: 0.8001 (t0) REVERT: A 65 PHE cc_start: 0.8160 (m-80) cc_final: 0.7866 (m-80) REVERT: A 104 TRP cc_start: 0.8297 (m-90) cc_final: 0.7983 (m-10) REVERT: A 168 PHE cc_start: 0.7641 (t80) cc_final: 0.7330 (t80) REVERT: A 191 GLU cc_start: 0.8503 (mp0) cc_final: 0.8173 (mp0) REVERT: A 202 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8208 (ptpt) REVERT: A 224 GLU cc_start: 0.7429 (pp20) cc_final: 0.7039 (pp20) REVERT: A 228 ASP cc_start: 0.8222 (m-30) cc_final: 0.7819 (t0) REVERT: A 235 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 237 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7483 (ttp-110) REVERT: A 273 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.7922 (mmm-85) REVERT: A 298 GLU cc_start: 0.9039 (tt0) cc_final: 0.8472 (tm-30) REVERT: A 317 ASN cc_start: 0.8909 (m110) cc_final: 0.8475 (m-40) REVERT: A 323 THR cc_start: 0.8666 (p) cc_final: 0.8414 (p) REVERT: A 355 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8524 (mmm-85) REVERT: A 386 LYS cc_start: 0.9194 (mttp) cc_final: 0.8601 (mtmm) REVERT: A 424 LYS cc_start: 0.8522 (ptmt) cc_final: 0.8127 (ptmt) REVERT: A 457 ARG cc_start: 0.8664 (tpt90) cc_final: 0.8096 (tpt-90) REVERT: A 461 LEU cc_start: 0.8619 (mt) cc_final: 0.8252 (mp) REVERT: A 529 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8207 (tmtt) REVERT: A 530 SER cc_start: 0.8947 (m) cc_final: 0.8666 (t) REVERT: A 555 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 560 LEU cc_start: 0.8968 (mm) cc_final: 0.8266 (mm) REVERT: A 563 GLN cc_start: 0.8555 (mt0) cc_final: 0.8006 (mt0) REVERT: A 568 ASP cc_start: 0.7598 (t0) cc_final: 0.7233 (t0) REVERT: A 569 ILE cc_start: 0.8696 (mp) cc_final: 0.8368 (tp) REVERT: A 584 ILE cc_start: 0.8690 (mm) cc_final: 0.8026 (mt) REVERT: A 658 ASN cc_start: 0.8799 (t0) cc_final: 0.8548 (t0) REVERT: A 663 ASP cc_start: 0.8799 (t0) cc_final: 0.8211 (t0) REVERT: A 697 MET cc_start: 0.8829 (tpp) cc_final: 0.8522 (tpt) REVERT: A 773 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8099 (mm-30) REVERT: A 787 GLN cc_start: 0.8692 (mt0) cc_final: 0.8332 (mp10) REVERT: A 790 LYS cc_start: 0.9215 (tppt) cc_final: 0.8749 (tptp) REVERT: A 814 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8698 (mmmt) REVERT: A 820 ASP cc_start: 0.8948 (t0) cc_final: 0.8470 (m-30) REVERT: A 824 ASN cc_start: 0.9077 (t0) cc_final: 0.8761 (t0) REVERT: A 825 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8983 (mmmt) REVERT: A 858 LEU cc_start: 0.8790 (mt) cc_final: 0.8328 (pt) REVERT: A 868 GLU cc_start: 0.8537 (pm20) cc_final: 0.8322 (pm20) REVERT: A 869 MET cc_start: 0.8934 (mtm) cc_final: 0.8634 (ptp) REVERT: A 900 MET cc_start: 0.8610 (mtt) cc_final: 0.8178 (mtt) REVERT: A 904 TYR cc_start: 0.8053 (t80) cc_final: 0.7616 (t80) REVERT: A 921 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8662 (mmmm) REVERT: A 935 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 988 GLU cc_start: 0.8431 (mp0) cc_final: 0.8154 (pm20) REVERT: A 1111 GLU cc_start: 0.8272 (mp0) cc_final: 0.7751 (mp0) REVERT: A 1139 ASP cc_start: 0.8185 (t70) cc_final: 0.7628 (t0) REVERT: B 191 GLU cc_start: 0.7982 (mp0) cc_final: 0.7579 (mp0) REVERT: B 222 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 245 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6647 (t70) REVERT: B 297 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 309 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 535 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8192 (mmmt) REVERT: B 537 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8616 (mmtt) REVERT: B 557 LYS cc_start: 0.9360 (mttt) cc_final: 0.8968 (mmtt) REVERT: B 584 ILE cc_start: 0.8272 (mp) cc_final: 0.7964 (tp) REVERT: B 646 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8100 (mmp80) REVERT: B 675 GLN cc_start: 0.8070 (pp30) cc_final: 0.7770 (pp30) REVERT: B 697 MET cc_start: 0.8474 (ptm) cc_final: 0.7975 (ppp) REVERT: B 699 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 726 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.8455 (mp) REVERT: B 737 ASP cc_start: 0.8034 (p0) cc_final: 0.7777 (p0) REVERT: B 762 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 767 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 773 GLU cc_start: 0.8688 (tp30) cc_final: 0.8300 (tp30) REVERT: B 776 LYS cc_start: 0.9319 (tppt) cc_final: 0.8959 (tppt) REVERT: B 780 GLU cc_start: 0.8579 (pt0) cc_final: 0.8265 (pp20) REVERT: B 790 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8490 (mtmt) REVERT: B 819 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 868 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8255 (pp20) REVERT: B 869 MET cc_start: 0.9056 (mtt) cc_final: 0.8701 (mtt) REVERT: B 872 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8420 (tp-100) REVERT: B 886 TRP cc_start: 0.8800 (p90) cc_final: 0.8263 (p90) REVERT: B 947 LYS cc_start: 0.9044 (mttt) cc_final: 0.8749 (mtmt) REVERT: B 1002 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8472 (tp-100) REVERT: B 1010 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 1031 GLU cc_start: 0.8429 (tp30) cc_final: 0.7540 (tp30) REVERT: B 1038 LYS cc_start: 0.9075 (tppt) cc_final: 0.8833 (tppt) REVERT: B 1045 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8153 (tptt) REVERT: B 1117 THR cc_start: 0.8783 (m) cc_final: 0.8506 (p) REVERT: B 1123 SER cc_start: 0.8616 (t) cc_final: 0.8170 (p) REVERT: B 1135 ASN cc_start: 0.8624 (t0) cc_final: 0.8339 (t0) REVERT: C 64 TRP cc_start: 0.6897 (t60) cc_final: 0.6300 (t-100) REVERT: C 88 ASP cc_start: 0.8352 (m-30) cc_final: 0.7501 (p0) REVERT: C 92 PHE cc_start: 0.8359 (t80) cc_final: 0.8004 (t80) REVERT: C 119 ILE cc_start: 0.8911 (pt) cc_final: 0.8660 (pt) REVERT: C 170 TYR cc_start: 0.8598 (t80) cc_final: 0.8258 (t80) REVERT: C 190 ARG cc_start: 0.8832 (mtt180) cc_final: 0.8028 (mmt180) REVERT: C 192 PHE cc_start: 0.8045 (m-80) cc_final: 0.7760 (m-10) REVERT: C 216 LEU cc_start: 0.7305 (tt) cc_final: 0.7047 (mp) REVERT: C 275 PHE cc_start: 0.8404 (m-80) cc_final: 0.8040 (m-10) REVERT: C 294 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7785 (p0) REVERT: C 297 SER cc_start: 0.8718 (m) cc_final: 0.8382 (p) REVERT: C 304 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8837 (mmtt) REVERT: C 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: C 321 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8929 (mm-40) REVERT: C 347 PHE cc_start: 0.6863 (m-80) cc_final: 0.6435 (m-80) REVERT: C 378 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8180 (mmmm) REVERT: C 389 ASP cc_start: 0.8571 (m-30) cc_final: 0.8199 (p0) REVERT: C 390 LEU cc_start: 0.9091 (pp) cc_final: 0.8755 (pp) REVERT: C 408 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8664 (tmm-80) REVERT: C 457 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7728 (ttt90) REVERT: C 490 PHE cc_start: 0.8990 (t80) cc_final: 0.8480 (t80) REVERT: C 516 GLU cc_start: 0.7371 (pm20) cc_final: 0.6920 (pm20) REVERT: C 529 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8992 (mmmt) REVERT: C 558 LYS cc_start: 0.8734 (tptt) cc_final: 0.8408 (tptp) REVERT: C 559 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7790 (t80) REVERT: C 563 GLN cc_start: 0.8536 (mt0) cc_final: 0.7984 (mt0) REVERT: C 571 ASP cc_start: 0.8145 (t70) cc_final: 0.7689 (t0) REVERT: C 580 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8033 (tp40) REVERT: C 606 ASN cc_start: 0.8891 (t0) cc_final: 0.8525 (t0) REVERT: C 661 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 755 GLN cc_start: 0.8701 (mt0) cc_final: 0.8418 (mt0) REVERT: C 761 THR cc_start: 0.8836 (m) cc_final: 0.8379 (p) REVERT: C 765 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8138 (ttm-80) REVERT: C 773 GLU cc_start: 0.8785 (pt0) cc_final: 0.8088 (pp20) REVERT: C 776 LYS cc_start: 0.9053 (tppt) cc_final: 0.8605 (tppt) REVERT: C 779 GLN cc_start: 0.8946 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 808 ASP cc_start: 0.8550 (p0) cc_final: 0.8036 (p0) REVERT: C 819 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 860 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9228 (p) REVERT: C 902 MET cc_start: 0.9293 (mmm) cc_final: 0.9033 (mmm) REVERT: C 904 TYR cc_start: 0.8355 (m-80) cc_final: 0.7750 (m-10) REVERT: C 933 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8571 (ttmm) REVERT: C 935 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: C 979 ASP cc_start: 0.8697 (t0) cc_final: 0.8337 (t0) REVERT: C 1005 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 1010 GLN cc_start: 0.9009 (tp40) cc_final: 0.8297 (tp-100) REVERT: C 1014 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8686 (tpp80) REVERT: C 1019 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8295 (tpp80) REVERT: C 1038 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8457 (mmmm) REVERT: C 1073 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8793 (mmtt) REVERT: C 1111 GLU cc_start: 0.8280 (mp0) cc_final: 0.7988 (mp0) REVERT: C 1120 THR cc_start: 0.9024 (p) cc_final: 0.8743 (t) REVERT: C 1138 TYR cc_start: 0.8203 (t80) cc_final: 0.7503 (t80) outliers start: 76 outliers final: 53 residues processed: 509 average time/residue: 0.4917 time to fit residues: 380.3987 Evaluate side-chains 514 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 447 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 144 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 360 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096749 restraints weight = 61668.408| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.39 r_work: 0.3172 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 26239 Z= 0.478 Angle : 0.913 13.779 35819 Z= 0.469 Chirality : 0.052 0.384 4175 Planarity : 0.005 0.059 4553 Dihedral : 7.933 98.271 4426 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 3.06 % Allowed : 22.07 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3159 helix: 1.64 (0.20), residues: 669 sheet: -0.63 (0.19), residues: 681 loop : -1.43 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 104 HIS 0.011 0.002 HIS B1083 PHE 0.028 0.003 PHE B 92 TYR 0.028 0.003 TYR C 495 ARG 0.010 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.01024 ( 35) link_NAG-ASN : angle 3.17869 ( 105) link_BETA1-4 : bond 0.00487 ( 11) link_BETA1-4 : angle 1.67283 ( 33) hydrogen bonds : bond 0.05105 ( 870) hydrogen bonds : angle 6.09588 ( 2436) SS BOND : bond 0.00637 ( 41) SS BOND : angle 2.57411 ( 82) covalent geometry : bond 0.00966 (26150) covalent geometry : angle 0.88934 (35599) Misc. bond : bond 0.00093 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 460 time to evaluate : 2.677 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: A 52 GLN cc_start: 0.8793 (tt0) cc_final: 0.8407 (tm-30) REVERT: A 53 ASP cc_start: 0.8516 (t0) cc_final: 0.8189 (t0) REVERT: A 104 TRP cc_start: 0.8490 (m-90) cc_final: 0.8219 (m-10) REVERT: A 191 GLU cc_start: 0.8461 (mp0) cc_final: 0.8223 (mp0) REVERT: A 228 ASP cc_start: 0.8331 (m-30) cc_final: 0.7642 (p0) REVERT: A 235 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8941 (mm) REVERT: A 237 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7613 (ttp-110) REVERT: A 273 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8032 (mmm-85) REVERT: A 298 GLU cc_start: 0.9117 (tt0) cc_final: 0.8582 (tp30) REVERT: A 300 LYS cc_start: 0.9563 (mttt) cc_final: 0.9242 (mtpp) REVERT: A 317 ASN cc_start: 0.8959 (m110) cc_final: 0.8542 (m-40) REVERT: A 353 TRP cc_start: 0.9092 (p-90) cc_final: 0.8882 (p90) REVERT: A 355 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8457 (mmm-85) REVERT: A 386 LYS cc_start: 0.9262 (mttp) cc_final: 0.8817 (mtmm) REVERT: A 424 LYS cc_start: 0.8700 (ptmt) cc_final: 0.7971 (ptpp) REVERT: A 456 PHE cc_start: 0.8859 (m-80) cc_final: 0.8643 (m-80) REVERT: A 461 LEU cc_start: 0.8761 (mt) cc_final: 0.8215 (mp) REVERT: A 532 ASN cc_start: 0.9009 (p0) cc_final: 0.8592 (p0) REVERT: A 560 LEU cc_start: 0.9021 (mm) cc_final: 0.8422 (mm) REVERT: A 563 GLN cc_start: 0.8500 (mt0) cc_final: 0.7992 (mt0) REVERT: A 568 ASP cc_start: 0.7877 (t0) cc_final: 0.7491 (t0) REVERT: A 569 ILE cc_start: 0.8831 (mp) cc_final: 0.8500 (tp) REVERT: A 697 MET cc_start: 0.8887 (tpp) cc_final: 0.8594 (tpt) REVERT: A 773 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8336 (mm-30) REVERT: A 779 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 787 GLN cc_start: 0.8809 (mt0) cc_final: 0.8413 (mp10) REVERT: A 790 LYS cc_start: 0.9275 (tppt) cc_final: 0.8792 (tptp) REVERT: A 814 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8847 (mmmt) REVERT: A 820 ASP cc_start: 0.9059 (t0) cc_final: 0.8562 (m-30) REVERT: A 824 ASN cc_start: 0.9173 (t0) cc_final: 0.8852 (t0) REVERT: A 825 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8966 (mmmt) REVERT: A 858 LEU cc_start: 0.8923 (mt) cc_final: 0.8369 (pp) REVERT: A 900 MET cc_start: 0.8767 (mtt) cc_final: 0.8404 (mtt) REVERT: A 904 TYR cc_start: 0.8183 (t80) cc_final: 0.7725 (t80) REVERT: A 921 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8842 (mmmm) REVERT: A 935 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 1045 LYS cc_start: 0.8468 (tptp) cc_final: 0.8235 (tptt) REVERT: A 1107 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.7971 (ttm170) REVERT: A 1111 GLU cc_start: 0.8271 (mp0) cc_final: 0.7801 (mp0) REVERT: A 1139 ASP cc_start: 0.8606 (t70) cc_final: 0.8129 (t0) REVERT: B 189 LEU cc_start: 0.8215 (tp) cc_final: 0.7936 (tp) REVERT: B 191 GLU cc_start: 0.7999 (mp0) cc_final: 0.7429 (mp0) REVERT: B 222 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 245 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6767 (t70) REVERT: B 276 LEU cc_start: 0.8886 (tp) cc_final: 0.8551 (tp) REVERT: B 297 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 309 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 557 LYS cc_start: 0.9337 (mttt) cc_final: 0.8969 (mmtt) REVERT: B 568 ASP cc_start: 0.7930 (p0) cc_final: 0.7579 (p0) REVERT: B 584 ILE cc_start: 0.8480 (mp) cc_final: 0.8151 (tp) REVERT: B 646 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8237 (mmp80) REVERT: B 675 GLN cc_start: 0.8094 (pp30) cc_final: 0.7812 (pp30) REVERT: B 697 MET cc_start: 0.8624 (ptm) cc_final: 0.8061 (ppp) REVERT: B 726 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 737 ASP cc_start: 0.8040 (p0) cc_final: 0.7680 (p0) REVERT: B 756 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8388 (t80) REVERT: B 762 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 773 GLU cc_start: 0.8667 (tp30) cc_final: 0.8337 (tp30) REVERT: B 776 LYS cc_start: 0.9404 (tppt) cc_final: 0.9085 (tppt) REVERT: B 780 GLU cc_start: 0.8601 (pt0) cc_final: 0.8391 (pp20) REVERT: B 869 MET cc_start: 0.9099 (mtt) cc_final: 0.8699 (mtm) REVERT: B 947 LYS cc_start: 0.9122 (mttt) cc_final: 0.8905 (mtmt) REVERT: B 988 GLU cc_start: 0.8448 (mp0) cc_final: 0.7954 (mp0) REVERT: B 1002 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8503 (tm-30) REVERT: B 1010 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8723 (mm-40) REVERT: B 1031 GLU cc_start: 0.8459 (tp30) cc_final: 0.7733 (tp30) REVERT: B 1117 THR cc_start: 0.8902 (m) cc_final: 0.8694 (p) REVERT: B 1123 SER cc_start: 0.8812 (t) cc_final: 0.8407 (p) REVERT: B 1135 ASN cc_start: 0.8531 (t0) cc_final: 0.8206 (t0) REVERT: C 64 TRP cc_start: 0.7037 (t60) cc_final: 0.6448 (t-100) REVERT: C 88 ASP cc_start: 0.8626 (m-30) cc_final: 0.8032 (p0) REVERT: C 92 PHE cc_start: 0.8425 (t80) cc_final: 0.8217 (t80) REVERT: C 135 PHE cc_start: 0.8964 (m-10) cc_final: 0.8731 (p90) REVERT: C 168 PHE cc_start: 0.7961 (t80) cc_final: 0.7544 (t80) REVERT: C 170 TYR cc_start: 0.8570 (t80) cc_final: 0.7610 (t80) REVERT: C 193 VAL cc_start: 0.8332 (t) cc_final: 0.7981 (m) REVERT: C 217 PRO cc_start: 0.8937 (Cg_exo) cc_final: 0.8626 (Cg_endo) REVERT: C 237 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: C 275 PHE cc_start: 0.8567 (m-80) cc_final: 0.8216 (m-10) REVERT: C 294 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8260 (p0) REVERT: C 297 SER cc_start: 0.8885 (m) cc_final: 0.8567 (p) REVERT: C 314 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8808 (tm-30) REVERT: C 378 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8279 (mmmm) REVERT: C 389 ASP cc_start: 0.8678 (m-30) cc_final: 0.8312 (p0) REVERT: C 390 LEU cc_start: 0.9207 (pp) cc_final: 0.8662 (pp) REVERT: C 408 ARG cc_start: 0.9035 (ttp80) cc_final: 0.8591 (ttp80) REVERT: C 457 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7534 (ttt90) REVERT: C 462 LYS cc_start: 0.8704 (tptt) cc_final: 0.8322 (tptt) REVERT: C 489 TYR cc_start: 0.7691 (m-80) cc_final: 0.7366 (m-10) REVERT: C 490 PHE cc_start: 0.9028 (t80) cc_final: 0.8613 (t80) REVERT: C 529 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8997 (mmmt) REVERT: C 563 GLN cc_start: 0.8569 (mt0) cc_final: 0.7978 (mm-40) REVERT: C 571 ASP cc_start: 0.8140 (t70) cc_final: 0.7757 (t0) REVERT: C 606 ASN cc_start: 0.9063 (t0) cc_final: 0.8720 (t0) REVERT: C 755 GLN cc_start: 0.8770 (mt0) cc_final: 0.8506 (mp10) REVERT: C 761 THR cc_start: 0.8966 (m) cc_final: 0.8286 (p) REVERT: C 765 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8065 (ttm-80) REVERT: C 773 GLU cc_start: 0.8820 (pt0) cc_final: 0.8379 (pp20) REVERT: C 776 LYS cc_start: 0.9124 (tppt) cc_final: 0.8690 (tppt) REVERT: C 779 GLN cc_start: 0.9037 (tt0) cc_final: 0.8582 (tm-30) REVERT: C 808 ASP cc_start: 0.8672 (p0) cc_final: 0.8023 (p0) REVERT: C 819 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 902 MET cc_start: 0.9354 (mmm) cc_final: 0.9077 (mmm) REVERT: C 904 TYR cc_start: 0.8407 (m-80) cc_final: 0.7809 (m-10) REVERT: C 979 ASP cc_start: 0.8757 (t0) cc_final: 0.8432 (t0) REVERT: C 1005 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 1010 GLN cc_start: 0.9026 (tp40) cc_final: 0.8093 (tp40) REVERT: C 1038 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8572 (mmmm) REVERT: C 1073 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8809 (mmtm) REVERT: C 1125 ASN cc_start: 0.8392 (t0) cc_final: 0.8060 (t0) REVERT: C 1138 TYR cc_start: 0.8229 (t80) cc_final: 0.7414 (t80) REVERT: C 1139 ASP cc_start: 0.7983 (t0) cc_final: 0.7634 (t0) outliers start: 85 outliers final: 58 residues processed: 521 average time/residue: 0.4419 time to fit residues: 350.6277 Evaluate side-chains 515 residues out of total 2795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 448 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 301 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 270 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103558 restraints weight = 60379.912| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.59 r_work: 0.3271 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26239 Z= 0.158 Angle : 0.779 12.374 35819 Z= 0.388 Chirality : 0.048 0.395 4175 Planarity : 0.005 0.056 4553 Dihedral : 7.301 92.131 4424 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 2.27 % Allowed : 23.77 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3159 helix: 1.97 (0.21), residues: 668 sheet: -0.45 (0.19), residues: 671 loop : -1.30 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 104 HIS 0.006 0.001 HIS A1064 PHE 0.030 0.002 PHE B 92 TYR 0.034 0.001 TYR B 170 ARG 0.015 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 35) link_NAG-ASN : angle 2.77857 ( 105) link_BETA1-4 : bond 0.00384 ( 11) link_BETA1-4 : angle 1.29849 ( 33) hydrogen bonds : bond 0.03880 ( 870) hydrogen bonds : angle 5.70015 ( 2436) SS BOND : bond 0.00466 ( 41) SS BOND : angle 2.19282 ( 82) covalent geometry : bond 0.00356 (26150) covalent geometry : angle 0.75850 (35599) Misc. bond : bond 0.00112 ( 2) =============================================================================== Job complete usr+sys time: 15255.82 seconds wall clock time: 266 minutes 53.98 seconds (16013.98 seconds total)