Starting phenix.real_space_refine on Fri Mar 6 09:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635.map" model { file = "/net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v23_31635/03_2026/7v23_31635_neut.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 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 134 5.16 5 C 18814 2.51 5 N 4881 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29633 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7879 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 8011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8011 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 7917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7917 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 55, 'TRANS': 975} Chain breaks: 7 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'TYR:plan': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "T" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" 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 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.89, per 1000 atoms: 0.23 Number of scatterers: 29633 At special positions: 0 Unit cell: (195.48, 193.32, 192.24, 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 134 16.00 O 5804 8.00 N 4881 7.00 C 18814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.00 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 87 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM29085 O5 NAG H 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29141 O5 NAG K 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29113 O5 NAG J 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29323 O5 NAG A1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM29225 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG 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-ASN " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 67 sheets defined 22.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.664A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.519A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.355A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.700A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.793A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.668A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.576A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.827A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.594A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.640A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.874A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.619A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.110A 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 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.761A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.941A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.634A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.624A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.417A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.749A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.602A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.143A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.587A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) 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: 3.729A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.506A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.747A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.640A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.861A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 30 removed outlier: 3.566A pdb=" N SER O 30 " --> pdb=" O PHE O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 65 Processing helix chain 'O' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP O 107 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER O 108 " --> pdb=" O SER O 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR O 110 " --> pdb=" O TRP O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 30 removed outlier: 3.589A pdb=" N ASP P 29 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU P 82 " --> pdb=" O ALA P 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.567A pdb=" N SER Q 30 " --> pdb=" O PHE Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP Q 107 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER Q 108 " --> pdb=" O SER Q 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR Q 110 " --> pdb=" O TRP Q 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.590A pdb=" N ASP R 29 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU R 82 " --> pdb=" O ALA R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 30 removed outlier: 3.567A pdb=" N SER S 30 " --> pdb=" O PHE S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER S 108 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR S 110 " --> pdb=" O TRP S 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 30 removed outlier: 3.589A pdb=" N ASP T 29 " --> pdb=" O LYS T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU T 82 " --> pdb=" O ALA T 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.601A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.557A 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: 5.353A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 removed outlier: 10.237A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 160 removed outlier: 10.237A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.455A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.258A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.970A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.437A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.972A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.119A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.686A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.907A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 154 through 157 removed outlier: 4.765A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 157 removed outlier: 4.765A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.797A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.631A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.547A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.334A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.826A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.489A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.514A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.563A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.504A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.138A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.240A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.661A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.053A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.568A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG O 38 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU O 46 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL O 114 " --> pdb=" O THR O 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 18 through 20 removed outlier: 4.358A pdb=" N THR P 69 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER P 66 " --> pdb=" O THR P 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'Q' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET Q 34 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL Q 114 " --> pdb=" O THR Q 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 18 through 20 removed outlier: 4.359A pdb=" N THR R 69 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER R 66 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 44 through 47 removed outlier: 6.480A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 44 through 47 removed outlier: 6.480A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET S 34 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG S 38 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU S 46 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL S 114 " --> pdb=" O THR S 98 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 18 through 20 removed outlier: 4.359A pdb=" N THR T 69 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER T 66 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'T' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3210 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: 8.21 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 11594 1.38 - 1.61: 18527 1.61 - 1.84: 175 1.84 - 2.07: 5 2.07 - 2.30: 1 Bond restraints: 30302 Sorted by residual: bond pdb=" CB ASN A1074 " pdb=" CG ASN A1074 " ideal model delta sigma weight residual 1.516 2.305 -0.789 2.50e-02 1.60e+03 9.96e+02 bond pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 1.328 1.904 -0.576 2.10e-02 2.27e+03 7.53e+02 bond pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta sigma weight residual 1.527 1.804 -0.277 1.30e-02 5.92e+03 4.55e+02 bond pdb=" C GLU A1072 " pdb=" N LYS A1073 " ideal model delta sigma weight residual 1.332 1.522 -0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" N ASN A1074 " pdb=" CA ASN A1074 " ideal model delta sigma weight residual 1.459 1.621 -0.162 1.27e-02 6.20e+03 1.63e+02 ... (remaining 30297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 41135 6.64 - 13.27: 122 13.27 - 19.91: 19 19.91 - 26.54: 1 26.54 - 33.18: 3 Bond angle restraints: 41280 Sorted by residual: angle pdb=" C LYS T 52 " pdb=" N ARG T 53 " pdb=" CA ARG T 53 " ideal model delta sigma weight residual 122.06 155.24 -33.18 1.78e+00 3.16e-01 3.47e+02 angle pdb=" C LYS R 52 " pdb=" N ARG R 53 " pdb=" CA ARG R 53 " ideal model delta sigma weight residual 122.06 155.20 -33.14 1.78e+00 3.16e-01 3.47e+02 angle pdb=" C LYS P 52 " pdb=" N ARG P 53 " pdb=" CA ARG P 53 " ideal model delta sigma weight residual 122.06 155.12 -33.06 1.78e+00 3.16e-01 3.45e+02 angle pdb=" N GLU A1072 " pdb=" CA GLU A1072 " pdb=" C GLU A1072 " ideal model delta sigma weight residual 109.23 127.53 -18.30 1.55e+00 4.16e-01 1.39e+02 angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta sigma weight residual 110.37 128.75 -18.38 1.65e+00 3.67e-01 1.24e+02 ... (remaining 41275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16765 17.97 - 35.94: 1300 35.94 - 53.90: 423 53.90 - 71.87: 78 71.87 - 89.84: 47 Dihedral angle restraints: 18613 sinusoidal: 7677 harmonic: 10936 Sorted by residual: dihedral pdb=" N ASN A1074 " pdb=" C ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta harmonic sigma weight residual 122.80 157.98 -35.18 0 2.50e+00 1.60e-01 1.98e+02 dihedral pdb=" C ASN A1074 " pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta harmonic sigma weight residual -122.60 -152.22 29.62 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" CA ASN A1074 " pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta harmonic sigma weight residual 180.00 122.51 57.49 0 5.00e+00 4.00e-02 1.32e+02 ... (remaining 18610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 4825 0.977 - 1.955: 2 1.955 - 2.932: 0 2.932 - 3.909: 0 3.909 - 4.887: 1 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 2.49 -4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CA ASN A1074 " pdb=" N ASN A1074 " pdb=" C ASN A1074 " pdb=" CB ASN A1074 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.05e+01 ... (remaining 4825 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.058 2.00e-02 2.50e+03 5.81e-02 4.21e+01 pdb=" CG ASN A 331 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.061 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.001 2.00e-02 2.50e+03 5.77e-02 4.17e+01 pdb=" CG ASN A 709 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 331 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ASN A 331 " 0.092 2.00e-02 2.50e+03 pdb=" O ASN A 331 " -0.035 2.00e-02 2.50e+03 pdb=" N ILE A 332 " -0.031 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 46 2.27 - 2.93: 13560 2.93 - 3.59: 41717 3.59 - 4.24: 67324 4.24 - 4.90: 114631 Nonbonded interactions: 237278 Sorted by model distance: nonbonded pdb=" ND2 ASN A1074 " pdb=" C5 NAG H 1 " model vdw 1.613 2.840 nonbonded pdb=" OE1 GLN C1071 " pdb=" O7 NAG L 1 " model vdw 1.944 3.040 nonbonded pdb=" OD2 ASP A 578 " pdb=" N THR A 581 " model vdw 1.986 3.120 nonbonded pdb=" CG ASN A1074 " pdb=" C5 NAG H 1 " model vdw 2.004 3.700 nonbonded pdb=" O SER Q 52 " pdb=" NH1 ARG Q 72 " model vdw 2.016 3.120 ... (remaining 237273 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 14 through 331 or (resid 332 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 344 or (resid 345 t \ hrough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 363 or (resid 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 373 or (res \ id 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thr \ ough 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 504 or (res \ id 505 and (name N or name CA or name C or name O or name CB )) or resid 506 thr \ ough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1307)) selection = (chain 'B' and (resid 14 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 426 or (resid 427 t \ hrough 428 and (name N or name CA or name C or name O or name CB )) or resid 429 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or resi \ d 503 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 throu \ gh 1307)) selection = (chain 'C' and (resid 14 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 454 or resid 491 th \ rough 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) \ or resid 506 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.500 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.011 0.789 30389 Z= 0.525 Angle : 1.334 57.304 41496 Z= 0.672 Chirality : 0.097 4.887 4828 Planarity : 0.007 0.091 5272 Dihedral : 15.052 89.841 11454 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.00 % Favored : 92.79 % Rotamer: Outliers : 3.68 % Allowed : 0.91 % Favored : 95.41 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3716 helix: 0.07 (0.19), residues: 736 sheet: -0.62 (0.17), residues: 903 loop : -1.52 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG A 319 TYR 0.041 0.002 TYR A 904 PHE 0.061 0.003 PHE A1075 TRP 0.065 0.004 TRP S 115 HIS 0.018 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.01066 (30302) covalent geometry : angle 1.15216 (41280) SS BOND : bond 0.00771 ( 45) SS BOND : angle 4.77699 ( 90) hydrogen bonds : bond 0.18166 ( 1142) hydrogen bonds : angle 8.61921 ( 3210) link_BETA1-4 : bond 0.01783 ( 10) link_BETA1-4 : angle 5.60621 ( 30) link_NAG-ASN : bond 0.07464 ( 32) link_NAG-ASN : angle 12.90821 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 440 time to evaluate : 1.044 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: B 150 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6406 (mmmm) REVERT: B 388 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.5399 (t0) REVERT: B 747 THR cc_start: 0.8074 (m) cc_final: 0.7525 (m) REVERT: B 751 ASN cc_start: 0.7571 (m-40) cc_final: 0.7317 (m110) REVERT: O 4 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3623 (mt) REVERT: O 57 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6253 (mp10) REVERT: O 112 MET cc_start: 0.7256 (mtp) cc_final: 0.6435 (ptt) REVERT: P 52 LYS cc_start: 0.8233 (mttt) cc_final: 0.7993 (mttp) REVERT: P 104 THR cc_start: 0.3513 (OUTLIER) cc_final: 0.3177 (p) REVERT: Q 73 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6363 (t70) REVERT: Q 80 TYR cc_start: 0.6749 (m-10) cc_final: 0.6501 (m-80) REVERT: Q 87 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5308 (mtm180) REVERT: R 62 SER cc_start: 0.7069 (OUTLIER) cc_final: 0.6649 (m) REVERT: R 74 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.4452 (mm) REVERT: R 80 MET cc_start: 0.6013 (mtp) cc_final: 0.5485 (tmt) outliers start: 117 outliers final: 12 residues processed: 500 average time/residue: 0.5182 time to fit residues: 315.9913 Evaluate side-chains 298 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 87 ARG Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain T residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 856 ASN B1005 GLN B1083 HIS B1088 HIS B1106 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 675 GLN C1005 GLN C1083 HIS C1135 ASN C1142 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116512 restraints weight = 59516.030| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.37 r_work: 0.3506 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 30389 Z= 0.198 Angle : 0.886 28.918 41496 Z= 0.420 Chirality : 0.069 2.421 4828 Planarity : 0.006 0.096 5272 Dihedral : 9.940 117.826 5073 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 2.67 % Allowed : 10.59 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3716 helix: 0.71 (0.20), residues: 699 sheet: -0.32 (0.17), residues: 970 loop : -1.21 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 87 TYR 0.022 0.002 TYR S 94 PHE 0.042 0.002 PHE A1075 TRP 0.033 0.002 TRP O 115 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00441 (30302) covalent geometry : angle 0.83762 (41280) SS BOND : bond 0.00608 ( 45) SS BOND : angle 2.72853 ( 90) hydrogen bonds : bond 0.04195 ( 1142) hydrogen bonds : angle 6.40608 ( 3210) link_BETA1-4 : bond 0.01313 ( 10) link_BETA1-4 : angle 4.27333 ( 30) link_NAG-ASN : bond 0.00654 ( 32) link_NAG-ASN : angle 5.02712 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 360 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 52 GLN cc_start: 0.8596 (pp30) cc_final: 0.8363 (tp40) REVERT: A 153 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7903 (tmm) REVERT: A 154 GLU cc_start: 0.7604 (tp30) cc_final: 0.6880 (tm-30) REVERT: A 224 GLU cc_start: 0.8511 (pt0) cc_final: 0.8277 (pt0) REVERT: A 329 PHE cc_start: 0.6479 (m-10) cc_final: 0.6218 (m-10) REVERT: A 581 THR cc_start: 0.7227 (t) cc_final: 0.6804 (p) REVERT: A 740 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6667 (ptm) REVERT: A 747 THR cc_start: 0.8132 (m) cc_final: 0.7470 (p) REVERT: A 751 ASN cc_start: 0.7521 (m-40) cc_final: 0.7304 (m110) REVERT: B 95 THR cc_start: 0.8096 (p) cc_final: 0.7830 (t) REVERT: B 747 THR cc_start: 0.8387 (m) cc_final: 0.7814 (m) REVERT: B 751 ASN cc_start: 0.8285 (m-40) cc_final: 0.7692 (m110) REVERT: B 794 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7800 (mm) REVERT: B 868 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: B 995 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8231 (mtp85) REVERT: B 1109 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: C 246 ARG cc_start: 0.6064 (mmt90) cc_final: 0.5471 (mmm-85) REVERT: C 646 ARG cc_start: 0.7816 (tpt170) cc_final: 0.7308 (tpt90) REVERT: C 661 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7828 (tm-30) REVERT: C 675 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6798 (tp40) REVERT: C 677 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7693 (mm-40) REVERT: C 751 ASN cc_start: 0.7957 (m-40) cc_final: 0.7584 (m110) REVERT: C 754 LEU cc_start: 0.8955 (mt) cc_final: 0.8705 (mt) REVERT: C 904 TYR cc_start: 0.6633 (t80) cc_final: 0.6212 (t80) REVERT: O 38 ARG cc_start: 0.3311 (mtt-85) cc_final: 0.2855 (mtt-85) REVERT: O 95 TYR cc_start: 0.5190 (m-10) cc_final: 0.4685 (m-10) REVERT: O 112 MET cc_start: 0.7050 (mtp) cc_final: 0.6756 (mtt) REVERT: P 48 TYR cc_start: 0.7184 (p90) cc_final: 0.6889 (p90) REVERT: P 52 LYS cc_start: 0.8113 (mttt) cc_final: 0.7518 (mmtp) REVERT: Q 32 TYR cc_start: 0.5821 (m-80) cc_final: 0.5311 (m-80) REVERT: Q 36 TRP cc_start: 0.4885 (m100) cc_final: 0.4039 (m100) REVERT: Q 87 ARG cc_start: 0.6291 (mmt-90) cc_final: 0.5388 (mmp-170) REVERT: Q 93 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7055 (t) REVERT: R 80 MET cc_start: 0.5969 (mtp) cc_final: 0.5370 (tmt) REVERT: S 29 PHE cc_start: 0.4817 (t80) cc_final: 0.4449 (t80) REVERT: S 45 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6076 (pt) REVERT: S 80 TYR cc_start: 0.4897 (m-80) cc_final: 0.4685 (m-80) REVERT: S 113 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.5923 (t70) REVERT: T 34 TRP cc_start: 0.4706 (m100) cc_final: 0.4474 (m100) outliers start: 85 outliers final: 28 residues processed: 420 average time/residue: 0.4846 time to fit residues: 251.8058 Evaluate side-chains 314 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain T residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 8 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 218 GLN B1005 GLN B1083 HIS B1088 HIS B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 901 GLN C 955 ASN C1083 HIS C1106 GLN P 68 ASN Q 35 ASN ** Q 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.162468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110086 restraints weight = 58374.368| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.32 r_work: 0.3408 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30389 Z= 0.190 Angle : 0.766 25.298 41496 Z= 0.374 Chirality : 0.060 1.981 4828 Planarity : 0.005 0.091 5272 Dihedral : 8.863 99.605 5040 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 3.11 % Allowed : 13.38 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3716 helix: 0.97 (0.20), residues: 697 sheet: -0.29 (0.17), residues: 948 loop : -1.14 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.025 0.002 TYR R 48 PHE 0.033 0.002 PHE O 29 TRP 0.042 0.002 TRP O 47 HIS 0.009 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00435 (30302) covalent geometry : angle 0.72485 (41280) SS BOND : bond 0.00985 ( 45) SS BOND : angle 2.44877 ( 90) hydrogen bonds : bond 0.03911 ( 1142) hydrogen bonds : angle 6.05422 ( 3210) link_BETA1-4 : bond 0.01354 ( 10) link_BETA1-4 : angle 3.69107 ( 30) link_NAG-ASN : bond 0.00704 ( 32) link_NAG-ASN : angle 4.21870 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 318 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7606 (tp30) cc_final: 0.6891 (tm-30) REVERT: A 224 GLU cc_start: 0.8521 (pt0) cc_final: 0.8305 (pt0) REVERT: A 329 PHE cc_start: 0.6822 (m-80) cc_final: 0.6585 (m-10) REVERT: A 1050 MET cc_start: 0.8948 (ptm) cc_final: 0.8605 (ptp) REVERT: A 1122 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (t) REVERT: B 95 THR cc_start: 0.8164 (p) cc_final: 0.7929 (t) REVERT: B 152 TRP cc_start: 0.4824 (OUTLIER) cc_final: 0.3536 (m100) REVERT: B 564 GLN cc_start: 0.6475 (pt0) cc_final: 0.6180 (pt0) REVERT: B 747 THR cc_start: 0.8401 (m) cc_final: 0.8094 (m) REVERT: B 751 ASN cc_start: 0.8443 (m-40) cc_final: 0.7997 (m110) REVERT: B 752 LEU cc_start: 0.8544 (tp) cc_final: 0.8174 (mp) REVERT: B 794 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 814 LYS cc_start: 0.8676 (mttp) cc_final: 0.8390 (mmtt) REVERT: B 868 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: B 995 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8286 (mtp85) REVERT: B 1109 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: C 200 TYR cc_start: 0.8076 (m-80) cc_final: 0.7155 (t80) REVERT: C 228 ASP cc_start: 0.7792 (t0) cc_final: 0.6046 (t0) REVERT: C 646 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7286 (tpt90) REVERT: C 751 ASN cc_start: 0.8218 (m-40) cc_final: 0.7949 (m-40) REVERT: C 904 TYR cc_start: 0.6847 (t80) cc_final: 0.6288 (t80) REVERT: O 95 TYR cc_start: 0.4821 (m-10) cc_final: 0.4435 (m-10) REVERT: O 115 TRP cc_start: 0.4825 (OUTLIER) cc_final: 0.3677 (t-100) REVERT: P 38 ARG cc_start: 0.6396 (mtp-110) cc_final: 0.5840 (ttm-80) REVERT: P 48 TYR cc_start: 0.7168 (p90) cc_final: 0.6858 (p90) REVERT: P 52 LYS cc_start: 0.8068 (mttt) cc_final: 0.7494 (mmtp) REVERT: P 85 TYR cc_start: 0.4459 (m-10) cc_final: 0.4195 (m-80) REVERT: Q 32 TYR cc_start: 0.6062 (m-80) cc_final: 0.5299 (m-80) REVERT: Q 87 ARG cc_start: 0.6250 (mmt-90) cc_final: 0.5521 (mmm160) REVERT: Q 93 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7079 (t) REVERT: Q 113 ASP cc_start: 0.2331 (OUTLIER) cc_final: 0.1702 (p0) REVERT: R 74 ILE cc_start: 0.4884 (pt) cc_final: 0.4650 (pp) REVERT: R 80 MET cc_start: 0.6055 (mtp) cc_final: 0.5394 (tmt) REVERT: S 45 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6207 (pt) REVERT: S 80 TYR cc_start: 0.4984 (m-80) cc_final: 0.4758 (m-80) REVERT: T 34 TRP cc_start: 0.4792 (m100) cc_final: 0.3591 (m-90) outliers start: 99 outliers final: 42 residues processed: 393 average time/residue: 0.4919 time to fit residues: 238.9773 Evaluate side-chains 306 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 33 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 349 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 422 ASN B 901 GLN B1005 GLN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN Q 103 HIS S 35 ASN S 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098232 restraints weight = 56521.514| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.76 r_work: 0.3251 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 30389 Z= 0.261 Angle : 0.832 29.191 41496 Z= 0.409 Chirality : 0.053 1.101 4828 Planarity : 0.006 0.106 5272 Dihedral : 8.377 104.377 5039 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 4.40 % Allowed : 15.68 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3716 helix: 0.57 (0.20), residues: 713 sheet: -0.43 (0.16), residues: 969 loop : -1.37 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 72 TYR 0.027 0.002 TYR C 904 PHE 0.043 0.003 PHE A1109 TRP 0.018 0.002 TRP C 436 HIS 0.015 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00625 (30302) covalent geometry : angle 0.80066 (41280) SS BOND : bond 0.00657 ( 45) SS BOND : angle 2.37280 ( 90) hydrogen bonds : bond 0.04052 ( 1142) hydrogen bonds : angle 6.00135 ( 3210) link_BETA1-4 : bond 0.01051 ( 10) link_BETA1-4 : angle 3.43169 ( 30) link_NAG-ASN : bond 0.00681 ( 32) link_NAG-ASN : angle 3.86147 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 313 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 133 PHE cc_start: 0.7910 (m-80) cc_final: 0.7569 (m-80) REVERT: A 135 PHE cc_start: 0.8341 (m-80) cc_final: 0.8134 (m-80) REVERT: A 154 GLU cc_start: 0.7584 (tp30) cc_final: 0.6989 (tm-30) REVERT: A 568 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7480 (p0) REVERT: A 985 ASP cc_start: 0.7499 (p0) cc_final: 0.7291 (p0) REVERT: A 987 PRO cc_start: 0.8759 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: A 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8902 (tpp) REVERT: B 40 ASP cc_start: 0.8362 (t0) cc_final: 0.8034 (p0) REVERT: B 100 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7353 (pp) REVERT: B 132 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7896 (mm-30) REVERT: B 152 TRP cc_start: 0.4900 (OUTLIER) cc_final: 0.3704 (m100) REVERT: B 515 PHE cc_start: 0.5286 (m-80) cc_final: 0.5054 (m-80) REVERT: B 564 GLN cc_start: 0.6544 (pt0) cc_final: 0.6235 (pt0) REVERT: B 582 LEU cc_start: 0.8853 (tt) cc_final: 0.8186 (mm) REVERT: B 794 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 814 LYS cc_start: 0.9010 (mttp) cc_final: 0.8604 (mmtt) REVERT: B 979 ASP cc_start: 0.8424 (t70) cc_final: 0.8042 (OUTLIER) REVERT: B 1005 GLN cc_start: 0.8886 (tt0) cc_final: 0.8513 (tt0) REVERT: C 133 PHE cc_start: 0.7349 (m-80) cc_final: 0.6750 (m-80) REVERT: C 200 TYR cc_start: 0.8263 (m-80) cc_final: 0.7665 (m-80) REVERT: C 228 ASP cc_start: 0.8272 (t0) cc_final: 0.7778 (t0) REVERT: C 329 PHE cc_start: 0.7013 (m-10) cc_final: 0.6755 (m-10) REVERT: C 378 LYS cc_start: 0.6952 (tppt) cc_final: 0.6725 (ttpt) REVERT: C 613 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8921 (mm-40) REVERT: C 646 ARG cc_start: 0.8571 (tpt170) cc_final: 0.7507 (tpt90) REVERT: C 677 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7850 (mm110) REVERT: C 964 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8434 (ttmm) REVERT: C 1130 ILE cc_start: 0.8786 (tp) cc_final: 0.8375 (mt) REVERT: O 29 PHE cc_start: 0.6271 (t80) cc_final: 0.5946 (t80) REVERT: O 34 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5974 (mmp) REVERT: O 95 TYR cc_start: 0.4769 (m-10) cc_final: 0.4163 (m-10) REVERT: O 115 TRP cc_start: 0.4255 (OUTLIER) cc_final: 0.2439 (t-100) REVERT: P 26 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7487 (ptpp) REVERT: P 48 TYR cc_start: 0.7123 (p90) cc_final: 0.6811 (p90) REVERT: P 52 LYS cc_start: 0.8125 (mttt) cc_final: 0.7648 (mttp) REVERT: Q 29 PHE cc_start: 0.5822 (t80) cc_final: 0.5167 (t80) REVERT: Q 32 TYR cc_start: 0.6172 (m-80) cc_final: 0.5496 (m-80) REVERT: Q 87 ARG cc_start: 0.6120 (mmt-90) cc_final: 0.5371 (mmm160) REVERT: Q 93 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7193 (t) REVERT: Q 113 ASP cc_start: 0.2354 (OUTLIER) cc_final: 0.1696 (p0) REVERT: S 80 TYR cc_start: 0.4895 (m-80) cc_final: 0.4587 (m-80) REVERT: T 34 TRP cc_start: 0.4826 (m100) cc_final: 0.4499 (m100) REVERT: T 60 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6232 (ptp-170) outliers start: 140 outliers final: 57 residues processed: 426 average time/residue: 0.5175 time to fit residues: 272.6604 Evaluate side-chains 312 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 26 LYS Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 340 optimal weight: 0.5980 chunk 334 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 347 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1142 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 239 GLN B 422 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 926 GLN C 992 GLN C1071 GLN C1083 HIS ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN P 78 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.154418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099972 restraints weight = 56752.262| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.76 r_work: 0.3282 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 30389 Z= 0.149 Angle : 0.689 18.378 41496 Z= 0.337 Chirality : 0.050 1.180 4828 Planarity : 0.005 0.087 5272 Dihedral : 7.798 96.419 5038 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.36 % Allowed : 19.01 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3716 helix: 1.08 (0.21), residues: 683 sheet: -0.40 (0.16), residues: 986 loop : -1.17 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1107 TYR 0.023 0.001 TYR C1138 PHE 0.027 0.001 PHE B 106 TRP 0.017 0.001 TRP C 436 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00342 (30302) covalent geometry : angle 0.65775 (41280) SS BOND : bond 0.00531 ( 45) SS BOND : angle 1.78433 ( 90) hydrogen bonds : bond 0.03431 ( 1142) hydrogen bonds : angle 5.75056 ( 3210) link_BETA1-4 : bond 0.01303 ( 10) link_BETA1-4 : angle 3.46978 ( 30) link_NAG-ASN : bond 0.00440 ( 32) link_NAG-ASN : angle 3.51583 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 283 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8453 (m) REVERT: A 52 GLN cc_start: 0.7921 (tp40) cc_final: 0.7592 (tp40) REVERT: A 135 PHE cc_start: 0.8035 (m-80) cc_final: 0.7778 (m-80) REVERT: A 154 GLU cc_start: 0.7546 (tp30) cc_final: 0.6976 (tm-30) REVERT: A 224 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 747 THR cc_start: 0.8120 (m) cc_final: 0.7905 (p) REVERT: A 748 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: A 780 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8293 (mm-30) REVERT: A 987 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: B 97 LYS cc_start: 0.8321 (pttm) cc_final: 0.7998 (tppt) REVERT: B 132 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8000 (mp0) REVERT: B 136 CYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4788 (m) REVERT: B 152 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.3778 (m100) REVERT: B 434 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.5044 (pt) REVERT: B 564 GLN cc_start: 0.6608 (pt0) cc_final: 0.6352 (pt0) REVERT: B 752 LEU cc_start: 0.8955 (tp) cc_final: 0.8673 (mp) REVERT: B 814 LYS cc_start: 0.9013 (mttp) cc_final: 0.8618 (mmtt) REVERT: B 1005 GLN cc_start: 0.8827 (tt0) cc_final: 0.8498 (tt0) REVERT: B 1092 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7935 (mt-10) REVERT: C 133 PHE cc_start: 0.7242 (m-80) cc_final: 0.6748 (m-80) REVERT: C 200 TYR cc_start: 0.7986 (m-80) cc_final: 0.7591 (m-80) REVERT: C 228 ASP cc_start: 0.8260 (t0) cc_final: 0.7829 (t0) REVERT: C 378 LYS cc_start: 0.6997 (tppt) cc_final: 0.6709 (ttpt) REVERT: C 646 ARG cc_start: 0.8568 (tpt170) cc_final: 0.7447 (tpt90) REVERT: C 677 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7798 (mm110) REVERT: C 752 LEU cc_start: 0.8835 (pp) cc_final: 0.8575 (pp) REVERT: C 1130 ILE cc_start: 0.8776 (tp) cc_final: 0.8385 (mt) REVERT: O 95 TYR cc_start: 0.4704 (m-10) cc_final: 0.3978 (m-10) REVERT: O 112 MET cc_start: 0.5561 (mtp) cc_final: 0.5154 (ptp) REVERT: O 115 TRP cc_start: 0.4802 (OUTLIER) cc_final: 0.2737 (t-100) REVERT: P 35 TYR cc_start: 0.5144 (m-80) cc_final: 0.4425 (m-80) REVERT: P 48 TYR cc_start: 0.7102 (p90) cc_final: 0.6884 (p90) REVERT: P 52 LYS cc_start: 0.8119 (mttt) cc_final: 0.7654 (mttp) REVERT: Q 29 PHE cc_start: 0.5809 (t80) cc_final: 0.5162 (t80) REVERT: Q 32 TYR cc_start: 0.6264 (m-80) cc_final: 0.5563 (m-80) REVERT: Q 87 ARG cc_start: 0.6448 (mmt-90) cc_final: 0.5600 (mmm160) REVERT: Q 93 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7238 (t) REVERT: Q 113 ASP cc_start: 0.2205 (OUTLIER) cc_final: 0.1437 (p0) REVERT: S 80 TYR cc_start: 0.4764 (m-80) cc_final: 0.4481 (m-80) REVERT: T 34 TRP cc_start: 0.4766 (m100) cc_final: 0.4473 (m100) REVERT: T 41 GLN cc_start: 0.5409 (mt0) cc_final: 0.4761 (mp10) REVERT: T 48 TYR cc_start: 0.3864 (p90) cc_final: 0.3586 (p90) outliers start: 107 outliers final: 41 residues processed: 371 average time/residue: 0.5461 time to fit residues: 248.4555 Evaluate side-chains 293 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 5 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 207 HIS B 211 ASN B 901 GLN B 935 GLN B1101 HIS C 245 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1106 GLN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN P 78 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.154069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099701 restraints weight = 56379.615| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.74 r_work: 0.3278 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30389 Z= 0.145 Angle : 0.682 28.823 41496 Z= 0.331 Chirality : 0.079 4.319 4828 Planarity : 0.005 0.107 5272 Dihedral : 7.098 76.903 5038 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 3.39 % Allowed : 19.57 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 3716 helix: 1.20 (0.20), residues: 694 sheet: -0.36 (0.15), residues: 996 loop : -1.14 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1107 TYR 0.040 0.001 TYR C 904 PHE 0.030 0.001 PHE A 106 TRP 0.016 0.001 TRP Q 115 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00336 (30302) covalent geometry : angle 0.65635 (41280) SS BOND : bond 0.00471 ( 45) SS BOND : angle 1.80907 ( 90) hydrogen bonds : bond 0.03341 ( 1142) hydrogen bonds : angle 5.58341 ( 3210) link_BETA1-4 : bond 0.01243 ( 10) link_BETA1-4 : angle 2.92818 ( 30) link_NAG-ASN : bond 0.00898 ( 32) link_NAG-ASN : angle 3.20082 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 266 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7941 (tp40) cc_final: 0.7589 (tp40) REVERT: A 109 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 154 GLU cc_start: 0.7569 (tp30) cc_final: 0.7040 (tm-30) REVERT: A 224 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7232 (pp20) REVERT: A 748 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 780 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8269 (mm-30) REVERT: A 912 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8831 (p) REVERT: A 1050 MET cc_start: 0.9039 (ptp) cc_final: 0.8711 (ptp) REVERT: B 79 PHE cc_start: 0.6635 (m-10) cc_final: 0.6425 (m-10) REVERT: B 97 LYS cc_start: 0.8227 (pttm) cc_final: 0.8006 (tptp) REVERT: B 132 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 136 CYS cc_start: 0.5165 (OUTLIER) cc_final: 0.4738 (m) REVERT: B 152 TRP cc_start: 0.4984 (OUTLIER) cc_final: 0.3779 (m100) REVERT: B 387 LEU cc_start: 0.8321 (mt) cc_final: 0.8119 (mp) REVERT: B 388 ASN cc_start: 0.7392 (m-40) cc_final: 0.6519 (t0) REVERT: B 564 GLN cc_start: 0.6602 (pt0) cc_final: 0.6332 (pt0) REVERT: B 614 ASP cc_start: 0.8388 (m-30) cc_final: 0.7882 (p0) REVERT: B 814 LYS cc_start: 0.8999 (mttp) cc_final: 0.8622 (mmtt) REVERT: B 990 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 1005 GLN cc_start: 0.8830 (tt0) cc_final: 0.8527 (tt0) REVERT: B 1092 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7938 (mt-10) REVERT: C 83 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 133 PHE cc_start: 0.7360 (m-80) cc_final: 0.6702 (m-80) REVERT: C 200 TYR cc_start: 0.7983 (m-80) cc_final: 0.7598 (m-80) REVERT: C 228 ASP cc_start: 0.8306 (t0) cc_final: 0.7879 (t0) REVERT: C 242 LEU cc_start: 0.8052 (mt) cc_final: 0.7718 (mt) REVERT: C 310 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9030 (ttmm) REVERT: C 378 LYS cc_start: 0.7152 (tppt) cc_final: 0.6886 (ttpt) REVERT: C 646 ARG cc_start: 0.8519 (tpt170) cc_final: 0.7437 (tpt90) REVERT: C 677 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7783 (mm110) REVERT: C 1130 ILE cc_start: 0.8870 (tp) cc_final: 0.8494 (mt) REVERT: O 59 TYR cc_start: 0.6202 (m-80) cc_final: 0.5922 (m-10) REVERT: O 95 TYR cc_start: 0.4712 (m-10) cc_final: 0.3747 (m-10) REVERT: O 115 TRP cc_start: 0.4799 (OUTLIER) cc_final: 0.2733 (t-100) REVERT: P 2 TYR cc_start: 0.3757 (t80) cc_final: 0.3407 (t80) REVERT: P 34 TRP cc_start: 0.4946 (m100) cc_final: 0.4367 (m100) REVERT: P 48 TYR cc_start: 0.7169 (p90) cc_final: 0.6895 (p90) REVERT: Q 29 PHE cc_start: 0.5768 (t80) cc_final: 0.5155 (t80) REVERT: Q 32 TYR cc_start: 0.6292 (m-80) cc_final: 0.5620 (m-80) REVERT: Q 73 ASP cc_start: 0.6586 (m-30) cc_final: 0.5168 (p0) REVERT: Q 87 ARG cc_start: 0.6255 (mmt-90) cc_final: 0.5458 (mmm160) REVERT: Q 93 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7171 (t) REVERT: Q 113 ASP cc_start: 0.2752 (OUTLIER) cc_final: 0.2083 (p0) REVERT: S 80 TYR cc_start: 0.4797 (m-80) cc_final: 0.4512 (m-80) REVERT: T 34 TRP cc_start: 0.4769 (m100) cc_final: 0.4494 (m100) REVERT: T 41 GLN cc_start: 0.5497 (mt0) cc_final: 0.4852 (mp10) outliers start: 108 outliers final: 54 residues processed: 360 average time/residue: 0.5329 time to fit residues: 235.4849 Evaluate side-chains 303 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 187 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 310 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 195 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1083 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 901 GLN B 920 GLN B1101 HIS C 245 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1106 GLN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.153150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098748 restraints weight = 56350.249| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.72 r_work: 0.3262 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 30389 Z= 0.165 Angle : 0.690 18.520 41496 Z= 0.338 Chirality : 0.076 4.086 4828 Planarity : 0.005 0.069 5272 Dihedral : 6.880 66.815 5038 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.46 % Allowed : 20.08 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.13), residues: 3716 helix: 1.20 (0.20), residues: 695 sheet: -0.25 (0.16), residues: 964 loop : -1.14 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1107 TYR 0.029 0.001 TYR C 904 PHE 0.030 0.002 PHE B 106 TRP 0.016 0.001 TRP B 436 HIS 0.030 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00387 (30302) covalent geometry : angle 0.66047 (41280) SS BOND : bond 0.00543 ( 45) SS BOND : angle 2.16772 ( 90) hydrogen bonds : bond 0.03343 ( 1142) hydrogen bonds : angle 5.59573 ( 3210) link_BETA1-4 : bond 0.01143 ( 10) link_BETA1-4 : angle 3.24319 ( 30) link_NAG-ASN : bond 0.01086 ( 32) link_NAG-ASN : angle 3.23624 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 252 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7936 (tp40) cc_final: 0.7562 (tp40) REVERT: A 109 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 135 PHE cc_start: 0.8057 (m-80) cc_final: 0.7733 (m-80) REVERT: A 154 GLU cc_start: 0.7555 (tp30) cc_final: 0.7019 (tm-30) REVERT: A 224 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: A 651 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 748 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: A 780 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8328 (mm-30) REVERT: A 1050 MET cc_start: 0.9029 (ptp) cc_final: 0.8772 (ptp) REVERT: B 132 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8109 (mp0) REVERT: B 152 TRP cc_start: 0.4979 (OUTLIER) cc_final: 0.3816 (m100) REVERT: B 388 ASN cc_start: 0.7541 (m-40) cc_final: 0.6715 (t0) REVERT: B 564 GLN cc_start: 0.6571 (pt0) cc_final: 0.6301 (pt0) REVERT: B 614 ASP cc_start: 0.8379 (m-30) cc_final: 0.7893 (p0) REVERT: B 814 LYS cc_start: 0.8986 (mttp) cc_final: 0.8612 (mmtt) REVERT: B 1005 GLN cc_start: 0.8840 (tt0) cc_final: 0.8536 (tt0) REVERT: B 1092 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7971 (mt-10) REVERT: C 83 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7807 (p) REVERT: C 133 PHE cc_start: 0.7379 (m-80) cc_final: 0.6738 (m-80) REVERT: C 200 TYR cc_start: 0.7957 (m-80) cc_final: 0.7604 (m-80) REVERT: C 228 ASP cc_start: 0.8243 (t0) cc_final: 0.7867 (t0) REVERT: C 310 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9007 (ttmm) REVERT: C 378 LYS cc_start: 0.7218 (tppt) cc_final: 0.6997 (ttpt) REVERT: C 564 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: C 646 ARG cc_start: 0.8567 (tpt170) cc_final: 0.7454 (tpt90) REVERT: C 677 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7787 (mm110) REVERT: C 918 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: C 964 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8410 (mppt) REVERT: C 1130 ILE cc_start: 0.8908 (tp) cc_final: 0.8563 (mt) REVERT: O 34 MET cc_start: 0.6254 (mmp) cc_final: 0.5942 (mmm) REVERT: O 68 PHE cc_start: 0.4418 (m-10) cc_final: 0.3635 (m-10) REVERT: O 83 MET cc_start: 0.1829 (tpp) cc_final: 0.0873 (mtp) REVERT: O 95 TYR cc_start: 0.4968 (m-10) cc_final: 0.3553 (m-80) REVERT: O 115 TRP cc_start: 0.4719 (OUTLIER) cc_final: 0.2516 (t-100) REVERT: P 2 TYR cc_start: 0.3713 (t80) cc_final: 0.3416 (t80) REVERT: P 34 TRP cc_start: 0.4948 (m100) cc_final: 0.4427 (m100) REVERT: Q 29 PHE cc_start: 0.5728 (t80) cc_final: 0.5137 (t80) REVERT: Q 32 TYR cc_start: 0.6213 (m-80) cc_final: 0.5541 (m-80) REVERT: Q 73 ASP cc_start: 0.6696 (m-30) cc_final: 0.5289 (p0) REVERT: Q 87 ARG cc_start: 0.6247 (mmt-90) cc_final: 0.5696 (ptt90) REVERT: Q 93 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7125 (t) REVERT: Q 113 ASP cc_start: 0.2640 (OUTLIER) cc_final: 0.1955 (p0) REVERT: R 16 GLN cc_start: 0.3218 (OUTLIER) cc_final: 0.2938 (mt0) REVERT: S 45 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5878 (mp) REVERT: S 80 TYR cc_start: 0.4871 (m-80) cc_final: 0.4584 (m-80) REVERT: T 34 TRP cc_start: 0.4832 (m100) cc_final: 0.4552 (m100) REVERT: T 41 GLN cc_start: 0.5469 (mt0) cc_final: 0.4837 (mp10) outliers start: 110 outliers final: 61 residues processed: 346 average time/residue: 0.5373 time to fit residues: 228.4517 Evaluate side-chains 308 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 366 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 186 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1088 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 690 GLN B 901 GLN B 919 ASN B 920 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 245 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1088 HIS C1135 ASN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 68 ASN R 41 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095855 restraints weight = 56279.408| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.86 r_work: 0.3219 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 30389 Z= 0.213 Angle : 0.728 20.840 41496 Z= 0.359 Chirality : 0.075 3.923 4828 Planarity : 0.005 0.086 5272 Dihedral : 6.800 65.766 5038 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.33 % Rotamer: Outliers : 3.24 % Allowed : 20.70 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3716 helix: 0.99 (0.20), residues: 706 sheet: -0.32 (0.16), residues: 967 loop : -1.14 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 60 TYR 0.036 0.002 TYR C 904 PHE 0.033 0.002 PHE A 759 TRP 0.019 0.002 TRP S 115 HIS 0.012 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00512 (30302) covalent geometry : angle 0.69621 (41280) SS BOND : bond 0.00449 ( 45) SS BOND : angle 2.21186 ( 90) hydrogen bonds : bond 0.03608 ( 1142) hydrogen bonds : angle 5.64476 ( 3210) link_BETA1-4 : bond 0.01153 ( 10) link_BETA1-4 : angle 3.41307 ( 30) link_NAG-ASN : bond 0.01039 ( 32) link_NAG-ASN : angle 3.56716 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 250 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8014 (tp40) cc_final: 0.7633 (tp40) REVERT: A 109 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (p) REVERT: A 135 PHE cc_start: 0.7974 (m-80) cc_final: 0.7669 (m-80) REVERT: A 154 GLU cc_start: 0.7557 (tp30) cc_final: 0.7047 (tm-30) REVERT: A 224 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: A 651 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 740 MET cc_start: 0.7863 (ttt) cc_final: 0.7551 (ttm) REVERT: A 748 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: A 780 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8389 (mm-30) REVERT: A 1092 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8273 (pt0) REVERT: B 79 PHE cc_start: 0.6623 (m-10) cc_final: 0.6420 (m-10) REVERT: B 132 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8183 (mp0) REVERT: B 152 TRP cc_start: 0.4954 (OUTLIER) cc_final: 0.3801 (m100) REVERT: B 388 ASN cc_start: 0.7990 (m-40) cc_final: 0.7320 (t0) REVERT: B 564 GLN cc_start: 0.6533 (pt0) cc_final: 0.6245 (pt0) REVERT: B 614 ASP cc_start: 0.8444 (m-30) cc_final: 0.7870 (p0) REVERT: B 814 LYS cc_start: 0.9002 (mttp) cc_final: 0.8622 (mmtt) REVERT: B 1092 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8042 (mt-10) REVERT: C 133 PHE cc_start: 0.7409 (m-80) cc_final: 0.6659 (m-80) REVERT: C 200 TYR cc_start: 0.7908 (m-80) cc_final: 0.7602 (m-80) REVERT: C 228 ASP cc_start: 0.8308 (t0) cc_final: 0.7986 (t0) REVERT: C 237 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6741 (mtp85) REVERT: C 310 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9013 (ttmm) REVERT: C 378 LYS cc_start: 0.7297 (tppt) cc_final: 0.7075 (ttpt) REVERT: C 388 ASN cc_start: 0.7623 (m110) cc_final: 0.7128 (t0) REVERT: C 646 ARG cc_start: 0.8586 (tpt170) cc_final: 0.7488 (tpt90) REVERT: C 677 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7798 (mm110) REVERT: C 918 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: C 964 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8480 (ttmm) REVERT: C 988 GLU cc_start: 0.8440 (pp20) cc_final: 0.8187 (pp20) REVERT: C 1040 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9073 (m) REVERT: C 1130 ILE cc_start: 0.8940 (tp) cc_final: 0.8723 (mt) REVERT: O 34 MET cc_start: 0.6348 (mmp) cc_final: 0.5853 (mmm) REVERT: O 59 TYR cc_start: 0.6375 (m-80) cc_final: 0.6052 (m-10) REVERT: O 83 MET cc_start: 0.1911 (tpp) cc_final: 0.1429 (tpp) REVERT: O 95 TYR cc_start: 0.5124 (m-10) cc_final: 0.3784 (m-80) REVERT: O 115 TRP cc_start: 0.4694 (OUTLIER) cc_final: 0.2471 (t-100) REVERT: P 2 TYR cc_start: 0.3484 (t80) cc_final: 0.3176 (t80) REVERT: P 34 TRP cc_start: 0.4921 (m100) cc_final: 0.4436 (m100) REVERT: P 52 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6837 (mmtp) REVERT: Q 29 PHE cc_start: 0.5726 (t80) cc_final: 0.5146 (t80) REVERT: Q 32 TYR cc_start: 0.6123 (m-80) cc_final: 0.5528 (m-80) REVERT: Q 73 ASP cc_start: 0.6726 (m-30) cc_final: 0.5333 (p0) REVERT: Q 87 ARG cc_start: 0.6466 (mmt-90) cc_final: 0.5864 (ptt90) REVERT: Q 93 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7198 (t) REVERT: Q 113 ASP cc_start: 0.2948 (OUTLIER) cc_final: 0.2340 (p0) REVERT: R 16 GLN cc_start: 0.3332 (OUTLIER) cc_final: 0.3034 (mt0) REVERT: S 45 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6006 (mp) REVERT: S 80 TYR cc_start: 0.4731 (m-80) cc_final: 0.4436 (m-80) REVERT: S 112 MET cc_start: 0.4360 (OUTLIER) cc_final: 0.4091 (mpt) REVERT: T 34 TRP cc_start: 0.4849 (m100) cc_final: 0.4603 (m100) REVERT: T 41 GLN cc_start: 0.5198 (mt0) cc_final: 0.4499 (mp10) outliers start: 103 outliers final: 58 residues processed: 337 average time/residue: 0.5377 time to fit residues: 222.8705 Evaluate side-chains 298 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 112 MET Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 365 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 350 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A1005 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 901 GLN B 992 GLN B1101 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** P 36 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.152269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097761 restraints weight = 55873.849| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.82 r_work: 0.3250 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30389 Z= 0.150 Angle : 0.684 22.268 41496 Z= 0.334 Chirality : 0.072 3.765 4828 Planarity : 0.004 0.053 5272 Dihedral : 6.504 65.240 5038 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.83 % Allowed : 21.39 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3716 helix: 1.14 (0.20), residues: 700 sheet: -0.24 (0.15), residues: 972 loop : -1.09 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 60 TYR 0.025 0.001 TYR C 904 PHE 0.033 0.001 PHE B 106 TRP 0.017 0.001 TRP B 436 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00349 (30302) covalent geometry : angle 0.65178 (41280) SS BOND : bond 0.00355 ( 45) SS BOND : angle 1.83524 ( 90) hydrogen bonds : bond 0.03294 ( 1142) hydrogen bonds : angle 5.52580 ( 3210) link_BETA1-4 : bond 0.01168 ( 10) link_BETA1-4 : angle 3.50740 ( 30) link_NAG-ASN : bond 0.00851 ( 32) link_NAG-ASN : angle 3.52877 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 250 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8007 (tp40) cc_final: 0.7622 (tp40) REVERT: A 81 ASN cc_start: 0.8344 (p0) cc_final: 0.7867 (p0) REVERT: A 109 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 124 THR cc_start: 0.8475 (p) cc_final: 0.8043 (t) REVERT: A 135 PHE cc_start: 0.7849 (m-80) cc_final: 0.7613 (m-80) REVERT: A 154 GLU cc_start: 0.7541 (tp30) cc_final: 0.7050 (tm-30) REVERT: A 224 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7061 (pp20) REVERT: A 651 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 748 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: A 780 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8414 (mm-30) REVERT: A 1050 MET cc_start: 0.9052 (ptp) cc_final: 0.8744 (ptp) REVERT: B 132 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8306 (mp0) REVERT: B 152 TRP cc_start: 0.4915 (OUTLIER) cc_final: 0.3788 (m100) REVERT: B 388 ASN cc_start: 0.8187 (m-40) cc_final: 0.7217 (t0) REVERT: B 564 GLN cc_start: 0.6475 (pt0) cc_final: 0.6215 (pt0) REVERT: B 614 ASP cc_start: 0.8440 (m-30) cc_final: 0.7924 (p0) REVERT: B 814 LYS cc_start: 0.8994 (mttp) cc_final: 0.8637 (mmtt) REVERT: B 1005 GLN cc_start: 0.8829 (tt0) cc_final: 0.8554 (mt0) REVERT: B 1092 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8088 (mt-10) REVERT: C 78 ARG cc_start: 0.7613 (ttm170) cc_final: 0.6539 (tpt90) REVERT: C 133 PHE cc_start: 0.7421 (m-80) cc_final: 0.6652 (m-80) REVERT: C 228 ASP cc_start: 0.8240 (t0) cc_final: 0.7965 (t0) REVERT: C 237 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6909 (mtp-110) REVERT: C 310 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8996 (ttmm) REVERT: C 646 ARG cc_start: 0.8570 (tpt170) cc_final: 0.7473 (tpt90) REVERT: C 690 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7744 (mm-40) REVERT: C 918 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 964 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8434 (mppt) REVERT: C 1040 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9103 (m) REVERT: C 1130 ILE cc_start: 0.8961 (tp) cc_final: 0.8729 (mt) REVERT: O 34 MET cc_start: 0.6614 (mmp) cc_final: 0.6357 (mmm) REVERT: O 39 GLN cc_start: 0.6095 (tp40) cc_final: 0.5793 (tp40) REVERT: O 59 TYR cc_start: 0.6453 (m-80) cc_final: 0.6111 (m-10) REVERT: O 83 MET cc_start: 0.2322 (tpp) cc_final: 0.1912 (tpp) REVERT: O 95 TYR cc_start: 0.5120 (m-10) cc_final: 0.3735 (m-80) REVERT: O 115 TRP cc_start: 0.4695 (OUTLIER) cc_final: 0.3430 (t-100) REVERT: P 2 TYR cc_start: 0.3365 (t80) cc_final: 0.3105 (t80) REVERT: P 34 TRP cc_start: 0.4847 (m100) cc_final: 0.4071 (m100) REVERT: P 35 TYR cc_start: 0.5134 (m-80) cc_final: 0.4890 (t80) REVERT: P 52 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6714 (mttp) REVERT: Q 29 PHE cc_start: 0.5854 (t80) cc_final: 0.5284 (t80) REVERT: Q 32 TYR cc_start: 0.6155 (m-80) cc_final: 0.5585 (m-80) REVERT: Q 73 ASP cc_start: 0.6747 (m-30) cc_final: 0.5365 (p0) REVERT: Q 87 ARG cc_start: 0.6441 (mmt-90) cc_final: 0.5846 (ptt90) REVERT: Q 93 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7174 (t) REVERT: Q 113 ASP cc_start: 0.2721 (OUTLIER) cc_final: 0.2090 (p0) REVERT: R 16 GLN cc_start: 0.3114 (OUTLIER) cc_final: 0.2847 (mt0) REVERT: S 80 TYR cc_start: 0.4800 (m-80) cc_final: 0.4455 (m-80) REVERT: S 112 MET cc_start: 0.4256 (OUTLIER) cc_final: 0.3937 (mpt) REVERT: T 34 TRP cc_start: 0.4842 (m100) cc_final: 0.4612 (m100) REVERT: T 41 GLN cc_start: 0.5176 (mt0) cc_final: 0.4476 (mp10) outliers start: 90 outliers final: 53 residues processed: 326 average time/residue: 0.4777 time to fit residues: 192.7736 Evaluate side-chains 295 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 112 MET Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 181 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 300 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 308 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 119 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 245 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1106 GLN ** P 36 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.152595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098202 restraints weight = 55864.034| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.86 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30389 Z= 0.140 Angle : 0.683 22.723 41496 Z= 0.333 Chirality : 0.070 3.667 4828 Planarity : 0.004 0.053 5272 Dihedral : 6.364 65.217 5038 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.39 % Allowed : 21.96 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3716 helix: 1.19 (0.20), residues: 700 sheet: -0.18 (0.16), residues: 963 loop : -1.05 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 60 TYR 0.025 0.001 TYR C 904 PHE 0.035 0.001 PHE A 106 TRP 0.018 0.001 TRP B 436 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00325 (30302) covalent geometry : angle 0.65250 (41280) SS BOND : bond 0.00434 ( 45) SS BOND : angle 1.64425 ( 90) hydrogen bonds : bond 0.03235 ( 1142) hydrogen bonds : angle 5.48231 ( 3210) link_BETA1-4 : bond 0.01159 ( 10) link_BETA1-4 : angle 3.51816 ( 30) link_NAG-ASN : bond 0.00794 ( 32) link_NAG-ASN : angle 3.49871 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 247 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8009 (tp40) cc_final: 0.7620 (tp40) REVERT: A 81 ASN cc_start: 0.8268 (p0) cc_final: 0.7779 (p0) REVERT: A 109 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 124 THR cc_start: 0.8359 (p) cc_final: 0.7915 (t) REVERT: A 135 PHE cc_start: 0.7752 (m-80) cc_final: 0.7490 (m-80) REVERT: A 154 GLU cc_start: 0.7442 (tp30) cc_final: 0.6976 (tm-30) REVERT: A 224 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 651 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 740 MET cc_start: 0.7625 (ttt) cc_final: 0.7418 (ttm) REVERT: A 748 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 780 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8405 (mm-30) REVERT: A 1050 MET cc_start: 0.9049 (ptp) cc_final: 0.8762 (ptp) REVERT: A 1092 GLU cc_start: 0.8453 (tp30) cc_final: 0.8207 (pt0) REVERT: A 1139 ASP cc_start: 0.7393 (m-30) cc_final: 0.7152 (t0) REVERT: B 78 ARG cc_start: 0.7301 (mtm110) cc_final: 0.6196 (ttp-110) REVERT: B 132 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8264 (mp0) REVERT: B 152 TRP cc_start: 0.4915 (OUTLIER) cc_final: 0.3812 (m100) REVERT: B 388 ASN cc_start: 0.8075 (m-40) cc_final: 0.7267 (t0) REVERT: B 564 GLN cc_start: 0.6565 (pt0) cc_final: 0.6296 (pt0) REVERT: B 614 ASP cc_start: 0.8459 (m-30) cc_final: 0.7926 (p0) REVERT: B 814 LYS cc_start: 0.8984 (mttp) cc_final: 0.8623 (mmtt) REVERT: B 1005 GLN cc_start: 0.8829 (tt0) cc_final: 0.8567 (mt0) REVERT: B 1092 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8104 (mt-10) REVERT: C 133 PHE cc_start: 0.7399 (m-80) cc_final: 0.6604 (m-80) REVERT: C 200 TYR cc_start: 0.8147 (m-80) cc_final: 0.7455 (t80) REVERT: C 237 ARG cc_start: 0.7227 (mtp180) cc_final: 0.6839 (mtp-110) REVERT: C 242 LEU cc_start: 0.8072 (mt) cc_final: 0.7764 (mt) REVERT: C 422 ASN cc_start: 0.6822 (t0) cc_final: 0.6394 (m110) REVERT: C 507 PRO cc_start: 0.6013 (Cg_exo) cc_final: 0.5719 (Cg_endo) REVERT: C 646 ARG cc_start: 0.8569 (tpt170) cc_final: 0.7435 (tpt90) REVERT: C 964 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8427 (mppt) REVERT: C 1040 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9107 (m) REVERT: C 1130 ILE cc_start: 0.8953 (tp) cc_final: 0.8716 (mt) REVERT: O 34 MET cc_start: 0.6607 (mmp) cc_final: 0.6321 (mmm) REVERT: O 39 GLN cc_start: 0.6232 (tp40) cc_final: 0.5873 (tp40) REVERT: O 59 TYR cc_start: 0.6441 (m-80) cc_final: 0.6091 (m-10) REVERT: O 83 MET cc_start: 0.1508 (tpp) cc_final: 0.1130 (tpp) REVERT: O 95 TYR cc_start: 0.5158 (m-10) cc_final: 0.3753 (m-80) REVERT: O 115 TRP cc_start: 0.4825 (OUTLIER) cc_final: 0.2517 (t-100) REVERT: P 34 TRP cc_start: 0.4821 (m100) cc_final: 0.4039 (m100) REVERT: P 52 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6905 (mmtp) REVERT: Q 29 PHE cc_start: 0.5835 (t80) cc_final: 0.5262 (t80) REVERT: Q 32 TYR cc_start: 0.6116 (m-80) cc_final: 0.5588 (m-80) REVERT: Q 73 ASP cc_start: 0.6790 (m-30) cc_final: 0.5360 (p0) REVERT: Q 87 ARG cc_start: 0.6487 (mmt-90) cc_final: 0.5915 (ptt90) REVERT: Q 93 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7193 (t) REVERT: Q 113 ASP cc_start: 0.3017 (OUTLIER) cc_final: 0.2613 (p0) REVERT: R 16 GLN cc_start: 0.3123 (OUTLIER) cc_final: 0.2859 (mt0) REVERT: S 38 ARG cc_start: 0.6675 (ptt180) cc_final: 0.6419 (ptt180) REVERT: S 80 TYR cc_start: 0.4855 (m-80) cc_final: 0.4471 (m-80) REVERT: S 112 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.3894 (mpt) REVERT: T 34 TRP cc_start: 0.4845 (m100) cc_final: 0.4631 (m100) REVERT: T 41 GLN cc_start: 0.5149 (mt0) cc_final: 0.4500 (mp10) outliers start: 76 outliers final: 50 residues processed: 313 average time/residue: 0.5191 time to fit residues: 200.1523 Evaluate side-chains 294 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 112 MET Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 321 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 14 GLN C 245 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.097868 restraints weight = 56084.024| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.85 r_work: 0.3250 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 30389 Z= 0.146 Angle : 0.682 23.255 41496 Z= 0.332 Chirality : 0.069 3.522 4828 Planarity : 0.004 0.080 5272 Dihedral : 6.310 65.813 5038 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.67 % Allowed : 21.77 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3716 helix: 1.10 (0.20), residues: 712 sheet: -0.22 (0.15), residues: 977 loop : -0.99 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 60 TYR 0.025 0.001 TYR C 904 PHE 0.036 0.001 PHE C 106 TRP 0.019 0.001 TRP B 436 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00342 (30302) covalent geometry : angle 0.65214 (41280) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.57719 ( 90) hydrogen bonds : bond 0.03245 ( 1142) hydrogen bonds : angle 5.47081 ( 3210) link_BETA1-4 : bond 0.01212 ( 10) link_BETA1-4 : angle 3.52716 ( 30) link_NAG-ASN : bond 0.00729 ( 32) link_NAG-ASN : angle 3.49132 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14581.12 seconds wall clock time: 248 minutes 2.11 seconds (14882.11 seconds total)