Starting phenix.real_space_refine on Sat Mar 7 09:16:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.map" model { file = "/net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e5r_30993/03_2026/7e5r_30993.cif" } resolution = 3.6 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= 0.001 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 168 5.16 5 C 25806 2.51 5 N 6759 2.21 5 O 7950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 241 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: 40683 Number of models: 1 Model: "" Number of chains: 36 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "O" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "T" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "S" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "Q" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 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: "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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.15, per 1000 atoms: 0.22 Number of scatterers: 40683 At special positions: 0 Unit cell: (217.36, 212.16, 206.96, 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 168 16.00 O 7950 8.00 N 6759 7.00 C 25806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 89 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 97 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG Y 1 " - " ASN A1098 " " NAG Z 1 " - " ASN A1134 " " NAG a 1 " - " ASN B 234 " " NAG b 1 " - " ASN B 717 " " NAG c 1 " - " ASN B 801 " " NAG d 1 " - " ASN B1098 " " NAG e 1 " - " ASN B1134 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9732 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 93 sheets defined 16.8% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN L 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN N 31 " --> pdb=" O SER N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN O 31 " --> pdb=" O SER O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.240A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.011A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.118A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.831A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.802A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.803A pdb=" N PHE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.801A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.241A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.010A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.742A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.119A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.832A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU R 84 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU W 32 " --> pdb=" O THR W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 66 removed outlier: 3.791A pdb=" N GLN W 66 " --> pdb=" O GLN W 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU S 84 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU X 32 " --> pdb=" O THR X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 66 removed outlier: 3.791A pdb=" N GLN X 66 " --> pdb=" O GLN X 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU Q 84 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU P 32 " --> pdb=" O THR P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 66 removed outlier: 3.790A pdb=" N GLN P 66 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.239A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.011A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.118A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.832A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL H 12 " --> pdb=" O GLU H 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 52 through 53 removed outlier: 5.504A pdb=" N SER H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS H 38 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 50 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.504A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.571A pdb=" N ILE N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL E 12 " --> pdb=" O GLU E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'E' and resid 52 through 53 removed outlier: 5.505A pdb=" N SER E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS E 38 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR O 50 " --> pdb=" O SER O 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 71 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 76 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.361A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.252A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.841A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.128A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1096 removed outlier: 4.820A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR M 113 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 59 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER M 52 " --> pdb=" O ASN M 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN M 57 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.302A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'T' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR T 113 " --> pdb=" O TYR T 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET T 34 " --> pdb=" O VAL T 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL T 50 " --> pdb=" O MET T 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR T 59 " --> pdb=" O VAL T 50 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER T 52 " --> pdb=" O ASN T 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN T 57 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.302A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR I 59 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER I 52 " --> pdb=" O ASN I 57 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN I 57 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.301A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 71 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 76 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF3, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.361A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 116 through 121 removed outlier: 4.252A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.581A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.841A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AF8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AG4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.129A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 1094 through 1096 removed outlier: 4.820A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL R 10 " --> pdb=" O THR R 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL R 34 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR R 50 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP R 36 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL R 10 " --> pdb=" O THR R 108 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 18 through 23 Processing sheet with id=AG9, first strand: chain 'W' and resid 3 through 4 Processing sheet with id=AH1, first strand: chain 'W' and resid 20 through 23 Processing sheet with id=AH2, first strand: chain 'W' and resid 46 through 49 Processing sheet with id=AH3, first strand: chain 'S' and resid 9 through 12 removed outlier: 6.573A pdb=" N VAL S 10 " --> pdb=" O THR S 108 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 9 through 12 removed outlier: 6.573A pdb=" N VAL S 10 " --> pdb=" O THR S 108 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AH6, first strand: chain 'X' and resid 3 through 4 Processing sheet with id=AH7, first strand: chain 'X' and resid 20 through 23 Processing sheet with id=AH8, first strand: chain 'X' and resid 46 through 49 Processing sheet with id=AH9, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL Q 10 " --> pdb=" O THR Q 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL Q 10 " --> pdb=" O THR Q 108 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 18 through 23 Processing sheet with id=AI3, first strand: chain 'P' and resid 3 through 4 Processing sheet with id=AI4, first strand: chain 'P' and resid 20 through 23 Processing sheet with id=AI5, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AI6, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.047A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.047A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER C 71 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AJ1, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.362A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 116 through 121 removed outlier: 4.253A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.840A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AJ6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AJ7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.818A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.818A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AK2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.129A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 4.819A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 3978 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: 11.08 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12926 1.34 - 1.46: 9129 1.46 - 1.58: 19348 1.58 - 1.70: 0 1.70 - 1.82: 219 Bond restraints: 41622 Sorted by residual: bond pdb=" N ASP N 102 " pdb=" CA ASP N 102 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.05e+01 bond pdb=" N ASP O 102 " pdb=" CA ASP O 102 " ideal model delta sigma weight residual 1.455 1.486 -0.031 7.00e-03 2.04e+04 1.97e+01 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 ... (remaining 41617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 54287 1.51 - 3.02: 1956 3.02 - 4.54: 327 4.54 - 6.05: 76 6.05 - 7.56: 18 Bond angle restraints: 56664 Sorted by residual: angle pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" C THR C 19 " ideal model delta sigma weight residual 112.88 107.08 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" N THR A 19 " pdb=" CA THR A 19 " pdb=" C THR A 19 " ideal model delta sigma weight residual 112.88 107.10 5.78 1.29e+00 6.01e-01 2.00e+01 angle pdb=" N THR B 19 " pdb=" CA THR B 19 " pdb=" C THR B 19 " ideal model delta sigma weight residual 112.88 107.11 5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" N TYR L 101 " pdb=" CA TYR L 101 " pdb=" C TYR L 101 " ideal model delta sigma weight residual 112.90 107.45 5.45 1.31e+00 5.83e-01 1.73e+01 angle pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 113.37 107.69 5.68 1.38e+00 5.25e-01 1.70e+01 ... (remaining 56659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 22637 17.77 - 35.55: 1929 35.55 - 53.32: 331 53.32 - 71.09: 77 71.09 - 88.87: 37 Dihedral angle restraints: 25011 sinusoidal: 9795 harmonic: 15216 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.86 -88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.82 -88.82 1 1.00e+01 1.00e-02 9.40e+01 ... (remaining 25008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5319 0.061 - 0.121: 1025 0.121 - 0.182: 100 0.182 - 0.243: 15 0.243 - 0.303: 3 Chirality restraints: 6462 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.68e+01 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.53e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.39e+01 ... (remaining 6459 not shown) Planarity restraints: 7293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG a 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG F 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " 0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG f 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " 0.086 2.00e-02 2.50e+03 ... (remaining 7290 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 474 2.54 - 3.13: 33300 3.13 - 3.72: 64626 3.72 - 4.31: 91699 4.31 - 4.90: 150412 Nonbonded interactions: 340511 Sorted by model distance: nonbonded pdb=" OD1 ASP L 102 " pdb=" CD PRO L 103 " model vdw 1.953 3.440 nonbonded pdb=" OD1 ASP O 102 " pdb=" CD PRO O 103 " model vdw 2.097 3.440 nonbonded pdb=" OD1 ASP N 102 " pdb=" CD PRO N 103 " model vdw 2.098 3.440 nonbonded pdb=" OG1 THR T 101 " pdb=" OE1 GLU B 484 " model vdw 2.195 3.040 nonbonded pdb=" O ARG B 214 " pdb=" OH TYR B 266 " model vdw 2.200 3.040 ... (remaining 340506 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 39.570 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.200 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41703 Z= 0.194 Angle : 0.685 7.561 56856 Z= 0.384 Chirality : 0.048 0.303 6462 Planarity : 0.008 0.303 7278 Dihedral : 13.498 86.060 15126 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.10 % Favored : 90.74 % Rotamer: Outliers : 0.37 % Allowed : 4.63 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.09), residues: 5196 helix: -0.83 (0.17), residues: 705 sheet: -2.68 (0.11), residues: 1374 loop : -3.38 (0.09), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.016 0.001 TYR A 145 PHE 0.018 0.001 PHE H 82 TRP 0.009 0.001 TRP O 110 HIS 0.009 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00353 (41622) covalent geometry : angle 0.68001 (56664) SS BOND : bond 0.00312 ( 51) SS BOND : angle 2.04414 ( 102) hydrogen bonds : bond 0.13391 ( 1482) hydrogen bonds : angle 8.69355 ( 3978) link_BETA1-4 : bond 0.00127 ( 15) link_BETA1-4 : angle 0.62875 ( 45) link_NAG-ASN : bond 0.00091 ( 15) link_NAG-ASN : angle 0.96271 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5133 (mmm) cc_final: 0.4633 (mtm) REVERT: A 780 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7312 (mt-10) REVERT: U 15 VAL cc_start: 0.2427 (OUTLIER) cc_final: 0.2103 (p) REVERT: B 153 MET cc_start: 0.9273 (tpt) cc_final: 0.8976 (tpt) REVERT: B 177 MET cc_start: 0.5427 (mmm) cc_final: 0.5033 (mtm) REVERT: B 1029 MET cc_start: 0.7854 (tpp) cc_final: 0.7650 (ttp) REVERT: W 33 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7046 (m) REVERT: W 65 PHE cc_start: 0.5392 (m-80) cc_final: 0.3815 (m-80) REVERT: W 71 MET cc_start: 0.2168 (mtm) cc_final: 0.0731 (mmm) REVERT: W 95 TYR cc_start: 0.6533 (m-80) cc_final: 0.5979 (m-80) REVERT: Q 88 TYR cc_start: 0.7479 (m-80) cc_final: 0.6847 (m-80) REVERT: P 30 LEU cc_start: 0.5443 (tp) cc_final: 0.5181 (tt) REVERT: P 71 MET cc_start: 0.2915 (mtm) cc_final: 0.0757 (mmm) REVERT: C 557 LYS cc_start: 0.4512 (mttt) cc_final: 0.4078 (mmtt) REVERT: C 780 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7171 (mt-10) outliers start: 16 outliers final: 4 residues processed: 301 average time/residue: 0.2756 time to fit residues: 130.7289 Evaluate side-chains 170 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 30.0000 chunk 516 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN N 6 GLN O 6 GLN A 81 ASN A 115 GLN A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 317 ASN A 334 ASN A 370 ASN A 487 ASN A 540 ASN A 655 HIS A 762 GLN A 804 GLN A 907 ASN A 935 GLN A 954 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN T 2 GLN T 111 GLN I 111 GLN B 81 ASN B 115 GLN B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 317 ASN B 334 ASN B 370 ASN B 487 ASN B 540 ASN B 655 HIS B 901 GLN B 907 ASN B 954 GLN B 955 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 32 ASN S 6 GLN S 32 ASN ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 GLN Q 6 GLN Q 32 ASN ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN P 114 GLN C 81 ASN C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 317 ASN C 334 ASN C 370 ASN C 487 ASN C 540 ASN C 655 HIS C 762 GLN C 901 GLN C 907 ASN C 954 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.095291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.065976 restraints weight = 282700.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066903 restraints weight = 148983.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.066341 restraints weight = 109074.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.066374 restraints weight = 111951.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.066441 restraints weight = 97069.178| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 41703 Z= 0.231 Angle : 0.695 12.620 56856 Z= 0.356 Chirality : 0.046 0.321 6462 Planarity : 0.005 0.091 7278 Dihedral : 5.480 49.628 6285 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.81 % Favored : 91.17 % Rotamer: Outliers : 1.44 % Allowed : 9.18 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.10), residues: 5196 helix: 0.47 (0.19), residues: 693 sheet: -2.33 (0.12), residues: 1404 loop : -2.90 (0.10), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 983 TYR 0.024 0.002 TYR X 61 PHE 0.023 0.002 PHE C 186 TRP 0.012 0.001 TRP P 48 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00505 (41622) covalent geometry : angle 0.69048 (56664) SS BOND : bond 0.00408 ( 51) SS BOND : angle 1.68107 ( 102) hydrogen bonds : bond 0.04403 ( 1482) hydrogen bonds : angle 7.19421 ( 3978) link_BETA1-4 : bond 0.00393 ( 15) link_BETA1-4 : angle 1.22061 ( 45) link_NAG-ASN : bond 0.00664 ( 15) link_NAG-ASN : angle 1.58347 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 31 ASN cc_start: 0.8474 (t0) cc_final: 0.8171 (p0) REVERT: A 177 MET cc_start: 0.5465 (mmm) cc_final: 0.4490 (mtm) REVERT: A 185 ASN cc_start: 0.5862 (t0) cc_final: 0.5451 (t0) REVERT: A 1029 MET cc_start: 0.8713 (tpp) cc_final: 0.8446 (ttp) REVERT: T 103 MET cc_start: 0.1042 (ptp) cc_final: -0.0311 (tpp) REVERT: K 92 TYR cc_start: 0.8132 (t80) cc_final: 0.7768 (t80) REVERT: B 177 MET cc_start: 0.5834 (mmm) cc_final: 0.5153 (mtm) REVERT: B 780 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 901 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: B 1029 MET cc_start: 0.8707 (tpp) cc_final: 0.8452 (ttp) REVERT: W 71 MET cc_start: 0.7906 (mtm) cc_final: 0.6647 (mmm) REVERT: X 39 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.6879 (mtt90) REVERT: X 61 TYR cc_start: 0.7829 (m-80) cc_final: 0.7527 (m-80) REVERT: X 65 PHE cc_start: 0.7367 (m-80) cc_final: 0.7000 (m-80) REVERT: X 71 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7251 (tpt) REVERT: X 109 PHE cc_start: 0.7875 (m-10) cc_final: 0.6479 (p90) REVERT: Q 88 TYR cc_start: 0.8669 (m-80) cc_final: 0.8428 (m-80) REVERT: C 557 LYS cc_start: 0.4527 (mttt) cc_final: 0.4209 (mmtt) REVERT: C 900 MET cc_start: 0.7626 (mtt) cc_final: 0.7384 (mtp) REVERT: C 902 MET cc_start: 0.8826 (tpt) cc_final: 0.8611 (tpt) outliers start: 63 outliers final: 27 residues processed: 236 average time/residue: 0.2553 time to fit residues: 98.5395 Evaluate side-chains 176 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain X residue 60 MET Chi-restraints excluded: chain X residue 71 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 743 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 287 optimal weight: 50.0000 chunk 282 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 292 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 420 optimal weight: 5.9990 chunk 277 optimal weight: 50.0000 chunk 55 optimal weight: 40.0000 chunk 115 optimal weight: 50.0000 chunk 476 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.093629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063512 restraints weight = 282298.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064042 restraints weight = 154374.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.063730 restraints weight = 104310.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.063877 restraints weight = 104799.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.063914 restraints weight = 94435.560| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 41703 Z= 0.395 Angle : 0.814 10.649 56856 Z= 0.413 Chirality : 0.049 0.247 6462 Planarity : 0.005 0.079 7278 Dihedral : 5.871 58.106 6280 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.97 % Allowed : 11.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.18 (0.11), residues: 5196 helix: 0.42 (0.19), residues: 702 sheet: -2.25 (0.12), residues: 1461 loop : -2.76 (0.10), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 55 TYR 0.063 0.002 TYR W 61 PHE 0.027 0.003 PHE A 306 TRP 0.016 0.002 TRP P 37 HIS 0.007 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00861 (41622) covalent geometry : angle 0.80520 (56664) SS BOND : bond 0.01047 ( 51) SS BOND : angle 2.36445 ( 102) hydrogen bonds : bond 0.04889 ( 1482) hydrogen bonds : angle 7.22873 ( 3978) link_BETA1-4 : bond 0.00612 ( 15) link_BETA1-4 : angle 1.76867 ( 45) link_NAG-ASN : bond 0.01395 ( 15) link_NAG-ASN : angle 2.34218 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 171 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6324 (t0) cc_final: 0.6074 (t0) REVERT: A 306 PHE cc_start: 0.5657 (p90) cc_final: 0.5228 (p90) REVERT: A 517 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 1029 MET cc_start: 0.8814 (tpp) cc_final: 0.8443 (ttp) REVERT: T 103 MET cc_start: 0.0368 (ptp) cc_final: 0.0094 (ptp) REVERT: K 92 TYR cc_start: 0.8380 (t80) cc_final: 0.8014 (t80) REVERT: B 177 MET cc_start: 0.6127 (mmm) cc_final: 0.5160 (mtm) REVERT: B 780 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 869 MET cc_start: 0.8800 (mtm) cc_final: 0.8491 (ttm) REVERT: B 1029 MET cc_start: 0.8850 (tpp) cc_final: 0.8488 (ttp) REVERT: W 39 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8620 (mtt90) REVERT: W 65 PHE cc_start: 0.6335 (m-80) cc_final: 0.6113 (m-80) REVERT: W 68 ARG cc_start: 0.7554 (ptm-80) cc_final: 0.6703 (ptm-80) REVERT: W 71 MET cc_start: 0.7659 (mtm) cc_final: 0.7339 (mmm) REVERT: W 82 MET cc_start: 0.5239 (ttt) cc_final: 0.4642 (ttt) REVERT: X 39 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7765 (mtt180) REVERT: X 61 TYR cc_start: 0.7844 (m-80) cc_final: 0.7552 (m-80) REVERT: X 71 MET cc_start: 0.7476 (mmm) cc_final: 0.7048 (tpt) REVERT: X 109 PHE cc_start: 0.8001 (m-10) cc_final: 0.7519 (m-10) REVERT: Q 88 TYR cc_start: 0.8574 (m-80) cc_final: 0.8317 (m-80) outliers start: 130 outliers final: 78 residues processed: 279 average time/residue: 0.2418 time to fit residues: 112.3003 Evaluate side-chains 226 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 147 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain X residue 60 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 297 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 40.0000 chunk 391 optimal weight: 30.0000 chunk 248 optimal weight: 0.9980 chunk 460 optimal weight: 40.0000 chunk 11 optimal weight: 30.0000 chunk 401 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 203 optimal weight: 50.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS A 901 GLN A 957 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 957 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN C 49 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 957 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.095199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.066666 restraints weight = 280397.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.067363 restraints weight = 154339.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.066325 restraints weight = 112963.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.066464 restraints weight = 118960.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066535 restraints weight = 95838.938| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41703 Z= 0.128 Angle : 0.610 10.449 56856 Z= 0.314 Chirality : 0.044 0.210 6462 Planarity : 0.004 0.067 7278 Dihedral : 5.252 55.834 6280 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.12 % Allowed : 13.81 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.11), residues: 5196 helix: 0.97 (0.19), residues: 693 sheet: -1.94 (0.12), residues: 1473 loop : -2.46 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 39 TYR 0.031 0.001 TYR W 61 PHE 0.022 0.001 PHE X 65 TRP 0.009 0.001 TRP L 110 HIS 0.005 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00277 (41622) covalent geometry : angle 0.60591 (56664) SS BOND : bond 0.00363 ( 51) SS BOND : angle 1.58035 ( 102) hydrogen bonds : bond 0.03853 ( 1482) hydrogen bonds : angle 6.46456 ( 3978) link_BETA1-4 : bond 0.00565 ( 15) link_BETA1-4 : angle 1.18805 ( 45) link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 1.14244 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 156 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.5420 (p90) cc_final: 0.5100 (p90) REVERT: A 1029 MET cc_start: 0.8622 (tpp) cc_final: 0.8417 (ttm) REVERT: U 92 TYR cc_start: 0.8145 (t80) cc_final: 0.7732 (m-80) REVERT: I 103 MET cc_start: 0.3368 (tpp) cc_final: 0.3052 (tpp) REVERT: K 92 TYR cc_start: 0.8380 (t80) cc_final: 0.8039 (t80) REVERT: B 177 MET cc_start: 0.5318 (mmm) cc_final: 0.5051 (mtm) REVERT: B 780 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 869 MET cc_start: 0.8572 (mtm) cc_final: 0.8284 (mtt) REVERT: B 1029 MET cc_start: 0.8669 (tpp) cc_final: 0.8340 (ttp) REVERT: W 39 ARG cc_start: 0.8937 (mtt90) cc_final: 0.8653 (mtt90) REVERT: W 68 ARG cc_start: 0.7210 (ptm-80) cc_final: 0.6732 (ptm-80) REVERT: W 71 MET cc_start: 0.8177 (mtm) cc_final: 0.7433 (tpp) REVERT: X 61 TYR cc_start: 0.7856 (m-80) cc_final: 0.7560 (m-80) REVERT: P 39 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7291 (mtt90) REVERT: P 47 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8097 (mp0) REVERT: P 49 MET cc_start: 0.8733 (ptt) cc_final: 0.8382 (ptp) REVERT: P 60 MET cc_start: 0.4245 (mtm) cc_final: 0.3419 (ttt) outliers start: 93 outliers final: 62 residues processed: 232 average time/residue: 0.2543 time to fit residues: 98.7118 Evaluate side-chains 206 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 0 optimal weight: 50.0000 chunk 505 optimal weight: 4.9990 chunk 483 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 469 optimal weight: 0.9990 chunk 403 optimal weight: 40.0000 chunk 512 optimal weight: 0.8980 chunk 447 optimal weight: 50.0000 chunk 496 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 471 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.094847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.066310 restraints weight = 280308.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.066555 restraints weight = 180364.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.066044 restraints weight = 121494.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.066068 restraints weight = 119104.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066181 restraints weight = 99221.783| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41703 Z= 0.146 Angle : 0.595 10.784 56856 Z= 0.304 Chirality : 0.043 0.183 6462 Planarity : 0.004 0.067 7278 Dihedral : 4.976 58.932 6280 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.44 % Allowed : 14.66 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.11), residues: 5196 helix: 1.16 (0.19), residues: 696 sheet: -1.65 (0.13), residues: 1455 loop : -2.33 (0.10), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 55 TYR 0.023 0.001 TYR W 61 PHE 0.019 0.001 PHE X 65 TRP 0.008 0.001 TRP O 110 HIS 0.005 0.001 HIS P 36 Details of bonding type rmsd covalent geometry : bond 0.00320 (41622) covalent geometry : angle 0.59074 (56664) SS BOND : bond 0.00320 ( 51) SS BOND : angle 1.47005 ( 102) hydrogen bonds : bond 0.03779 ( 1482) hydrogen bonds : angle 6.20707 ( 3978) link_BETA1-4 : bond 0.00451 ( 15) link_BETA1-4 : angle 1.10950 ( 45) link_NAG-ASN : bond 0.00426 ( 15) link_NAG-ASN : angle 1.26588 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 152 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.5467 (p90) cc_final: 0.5129 (p90) REVERT: A 1029 MET cc_start: 0.8653 (tpp) cc_final: 0.8415 (ttm) REVERT: T 103 MET cc_start: 0.0201 (ptp) cc_final: -0.1326 (tpp) REVERT: I 103 MET cc_start: 0.3206 (tpp) cc_final: 0.2977 (tpp) REVERT: K 92 TYR cc_start: 0.8396 (t80) cc_final: 0.8013 (t80) REVERT: B 177 MET cc_start: 0.5532 (mmm) cc_final: 0.5134 (mtm) REVERT: B 780 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 869 MET cc_start: 0.8608 (mtm) cc_final: 0.8238 (ttm) REVERT: B 1029 MET cc_start: 0.8676 (tpp) cc_final: 0.8299 (ttp) REVERT: W 68 ARG cc_start: 0.6936 (ptm-80) cc_final: 0.6724 (ptm-80) REVERT: W 71 MET cc_start: 0.7736 (mtm) cc_final: 0.6238 (tpt) REVERT: P 39 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7609 (mtt90) REVERT: P 47 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8132 (mp0) REVERT: P 49 MET cc_start: 0.8745 (ptt) cc_final: 0.8226 (ptt) REVERT: P 60 MET cc_start: 0.4288 (mtm) cc_final: 0.3280 (ttt) outliers start: 107 outliers final: 75 residues processed: 241 average time/residue: 0.2450 time to fit residues: 100.4152 Evaluate side-chains 219 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 144 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 307 optimal weight: 7.9990 chunk 113 optimal weight: 50.0000 chunk 268 optimal weight: 7.9990 chunk 389 optimal weight: 50.0000 chunk 57 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 214 optimal weight: 6.9990 chunk 398 optimal weight: 40.0000 chunk 300 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1142 GLN ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.092963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.062165 restraints weight = 280429.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.063126 restraints weight = 153753.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.062702 restraints weight = 108367.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062905 restraints weight = 93255.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.062756 restraints weight = 93663.891| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.121 41703 Z= 0.415 Angle : 0.815 15.028 56856 Z= 0.413 Chirality : 0.049 0.280 6462 Planarity : 0.005 0.063 7278 Dihedral : 5.678 55.418 6280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.88 % Allowed : 15.73 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -2.70 (0.11), residues: 5196 helix: 0.57 (0.19), residues: 708 sheet: -1.85 (0.12), residues: 1548 loop : -2.43 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 190 TYR 0.023 0.002 TYR A 789 PHE 0.029 0.002 PHE B 562 TRP 0.013 0.001 TRP D 93 HIS 0.008 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00902 (41622) covalent geometry : angle 0.80579 (56664) SS BOND : bond 0.01083 ( 51) SS BOND : angle 2.34366 ( 102) hydrogen bonds : bond 0.04705 ( 1482) hydrogen bonds : angle 6.85447 ( 3978) link_BETA1-4 : bond 0.00539 ( 15) link_BETA1-4 : angle 1.52898 ( 45) link_NAG-ASN : bond 0.01532 ( 15) link_NAG-ASN : angle 2.58085 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 150 time to evaluate : 1.520 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: H 9 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5379 (p90) REVERT: A 306 PHE cc_start: 0.5558 (p90) cc_final: 0.5315 (p90) REVERT: A 562 PHE cc_start: 0.4984 (OUTLIER) cc_final: 0.3485 (m-10) REVERT: A 1029 MET cc_start: 0.8826 (tpp) cc_final: 0.8467 (ttp) REVERT: U 92 TYR cc_start: 0.8374 (t80) cc_final: 0.8091 (m-80) REVERT: T 103 MET cc_start: 0.1507 (ptp) cc_final: 0.1218 (ptp) REVERT: I 103 MET cc_start: 0.3842 (tpp) cc_final: 0.3516 (tpp) REVERT: K 92 TYR cc_start: 0.8480 (t80) cc_final: 0.8250 (t80) REVERT: B 177 MET cc_start: 0.6084 (mmm) cc_final: 0.5091 (mtm) REVERT: B 780 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 869 MET cc_start: 0.8785 (mtm) cc_final: 0.8534 (ttm) REVERT: B 904 TYR cc_start: 0.8138 (m-10) cc_final: 0.7930 (m-10) REVERT: B 1029 MET cc_start: 0.8809 (tpp) cc_final: 0.8398 (ttp) REVERT: W 71 MET cc_start: 0.8313 (mtm) cc_final: 0.7858 (tpp) REVERT: W 82 MET cc_start: 0.5539 (ttt) cc_final: 0.4774 (mtt) REVERT: X 35 MET cc_start: 0.4869 (pmm) cc_final: 0.4623 (pmm) REVERT: X 60 MET cc_start: 0.5557 (ptt) cc_final: 0.5240 (ptt) REVERT: X 109 PHE cc_start: 0.8096 (m-10) cc_final: 0.7655 (m-80) REVERT: P 39 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7633 (mtt90) REVERT: P 47 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8300 (mp0) REVERT: P 60 MET cc_start: 0.5275 (mtm) cc_final: 0.4560 (ttt) REVERT: P 82 MET cc_start: 0.4137 (tpt) cc_final: 0.3427 (tpt) REVERT: C 1029 MET cc_start: 0.8871 (tpp) cc_final: 0.8635 (ttm) outliers start: 126 outliers final: 85 residues processed: 256 average time/residue: 0.2462 time to fit residues: 105.6563 Evaluate side-chains 226 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 139 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 133 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 329 optimal weight: 0.9990 chunk 212 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 207 optimal weight: 30.0000 chunk 320 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 343 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 901 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN B 185 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 121 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.064818 restraints weight = 279029.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.065156 restraints weight = 152127.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.065786 restraints weight = 109780.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.065271 restraints weight = 81070.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.065317 restraints weight = 65408.329| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41703 Z= 0.134 Angle : 0.604 11.365 56856 Z= 0.311 Chirality : 0.044 0.215 6462 Planarity : 0.004 0.065 7278 Dihedral : 5.164 52.528 6280 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.17 % Allowed : 16.85 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.11), residues: 5196 helix: 1.04 (0.19), residues: 696 sheet: -1.51 (0.13), residues: 1428 loop : -2.21 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 39 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE E 9 TRP 0.015 0.001 TRP X 37 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00294 (41622) covalent geometry : angle 0.59844 (56664) SS BOND : bond 0.00332 ( 51) SS BOND : angle 1.88340 ( 102) hydrogen bonds : bond 0.03799 ( 1482) hydrogen bonds : angle 6.22574 ( 3978) link_BETA1-4 : bond 0.00522 ( 15) link_BETA1-4 : angle 0.85899 ( 45) link_NAG-ASN : bond 0.00306 ( 15) link_NAG-ASN : angle 1.32886 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 156 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.6013 (OUTLIER) cc_final: 0.5139 (p90) REVERT: H 11 SER cc_start: 0.0077 (OUTLIER) cc_final: -0.0602 (m) REVERT: A 306 PHE cc_start: 0.5216 (p90) cc_final: 0.4997 (p90) REVERT: T 103 MET cc_start: 0.0782 (ptp) cc_final: 0.0510 (ptp) REVERT: I 103 MET cc_start: 0.3678 (tpp) cc_final: 0.3407 (tpp) REVERT: K 92 TYR cc_start: 0.8474 (t80) cc_final: 0.8214 (t80) REVERT: B 177 MET cc_start: 0.5367 (mmm) cc_final: 0.5141 (mtm) REVERT: B 780 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 1029 MET cc_start: 0.8719 (tpp) cc_final: 0.8408 (ttp) REVERT: R 87 TYR cc_start: 0.4062 (m-10) cc_final: 0.3740 (m-10) REVERT: W 68 ARG cc_start: 0.7040 (ptm-80) cc_final: 0.6040 (ptm-80) REVERT: W 71 MET cc_start: 0.8065 (mtm) cc_final: 0.6730 (tpp) REVERT: X 61 TYR cc_start: 0.7886 (m-10) cc_final: 0.7425 (m-80) REVERT: X 109 PHE cc_start: 0.8168 (m-10) cc_final: 0.7694 (m-80) REVERT: P 39 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7756 (mpt90) REVERT: P 49 MET cc_start: 0.8825 (ptt) cc_final: 0.8586 (ptp) REVERT: P 60 MET cc_start: 0.4930 (mtm) cc_final: 0.4095 (ttt) outliers start: 95 outliers final: 70 residues processed: 232 average time/residue: 0.2558 time to fit residues: 99.5372 Evaluate side-chains 213 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 141 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 962 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 501 optimal weight: 8.9990 chunk 51 optimal weight: 50.0000 chunk 359 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 505 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 chunk 409 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN E 99 GLN A 49 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN R 32 ASN ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 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 = 0.4340 r_free = 0.4340 target = 0.092611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063542 restraints weight = 280895.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.065187 restraints weight = 142653.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064693 restraints weight = 88599.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064693 restraints weight = 95661.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064693 restraints weight = 95661.570| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.129 41703 Z= 0.447 Angle : 0.855 12.743 56856 Z= 0.432 Chirality : 0.049 0.292 6462 Planarity : 0.005 0.062 7278 Dihedral : 5.897 46.874 6280 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.74 % Allowed : 16.78 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.65 (0.11), residues: 5196 helix: 0.48 (0.19), residues: 705 sheet: -1.80 (0.13), residues: 1530 loop : -2.37 (0.11), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 567 TYR 0.024 0.002 TYR A 789 PHE 0.040 0.003 PHE C 562 TRP 0.019 0.002 TRP W 37 HIS 0.009 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00973 (41622) covalent geometry : angle 0.84679 (56664) SS BOND : bond 0.00791 ( 51) SS BOND : angle 2.30386 ( 102) hydrogen bonds : bond 0.04814 ( 1482) hydrogen bonds : angle 6.86670 ( 3978) link_BETA1-4 : bond 0.00678 ( 15) link_BETA1-4 : angle 1.52540 ( 45) link_NAG-ASN : bond 0.01551 ( 15) link_NAG-ASN : angle 2.60082 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 149 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4686 (p90) REVERT: H 11 SER cc_start: 0.0007 (OUTLIER) cc_final: -0.0848 (m) REVERT: L 6 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7047 (mt0) REVERT: A 185 ASN cc_start: 0.7207 (t0) cc_final: 0.6942 (t0) REVERT: A 306 PHE cc_start: 0.5750 (p90) cc_final: 0.5535 (p90) REVERT: A 562 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.3573 (m-10) REVERT: M 103 MET cc_start: 0.1862 (tpp) cc_final: 0.1599 (tpp) REVERT: U 92 TYR cc_start: 0.8163 (t80) cc_final: 0.7883 (t80) REVERT: T 103 MET cc_start: -0.1810 (ptp) cc_final: -0.2295 (ptp) REVERT: K 92 TYR cc_start: 0.8311 (t80) cc_final: 0.7830 (t80) REVERT: B 127 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7871 (m) REVERT: B 306 PHE cc_start: 0.5700 (p90) cc_final: 0.5425 (p90) REVERT: B 562 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.2979 (m-10) REVERT: B 904 TYR cc_start: 0.7757 (m-10) cc_final: 0.7465 (m-10) REVERT: B 1029 MET cc_start: 0.8799 (tpp) cc_final: 0.8406 (ttp) REVERT: W 68 ARG cc_start: 0.6631 (ptm-80) cc_final: 0.6339 (tmt170) REVERT: W 71 MET cc_start: 0.5459 (mtm) cc_final: 0.4786 (tpp) REVERT: S 32 ASN cc_start: 0.6671 (m110) cc_final: 0.5766 (t0) REVERT: S 33 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6965 (m-10) REVERT: X 39 ARG cc_start: 0.7813 (mpt180) cc_final: 0.7242 (mpt180) REVERT: X 61 TYR cc_start: 0.7679 (m-10) cc_final: 0.7192 (m-10) REVERT: X 71 MET cc_start: 0.6704 (tpt) cc_final: 0.5695 (mmt) REVERT: X 109 PHE cc_start: 0.8190 (m-10) cc_final: 0.7767 (m-80) REVERT: P 71 MET cc_start: 0.5943 (mmm) cc_final: 0.5654 (mmm) REVERT: C 127 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8251 (m) REVERT: C 562 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.3711 (m-10) outliers start: 120 outliers final: 88 residues processed: 252 average time/residue: 0.2288 time to fit residues: 98.2254 Evaluate side-chains 236 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 139 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 82 MET Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain S residue 33 TYR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 GLN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 419 optimal weight: 0.7980 chunk 288 optimal weight: 30.0000 chunk 467 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 503 optimal weight: 0.9990 chunk 342 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN T 74 ASN V 37 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.063702 restraints weight = 279506.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.065087 restraints weight = 143021.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.064480 restraints weight = 93182.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.064591 restraints weight = 77191.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064477 restraints weight = 77676.309| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41703 Z= 0.147 Angle : 0.637 13.563 56856 Z= 0.326 Chirality : 0.044 0.228 6462 Planarity : 0.005 0.072 7278 Dihedral : 5.460 46.280 6280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.24 % Allowed : 17.53 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.11), residues: 5196 helix: 1.00 (0.19), residues: 696 sheet: -1.61 (0.13), residues: 1473 loop : -2.18 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 567 TYR 0.032 0.001 TYR R 33 PHE 0.020 0.001 PHE E 9 TRP 0.015 0.001 TRP W 37 HIS 0.008 0.001 HIS P 36 Details of bonding type rmsd covalent geometry : bond 0.00325 (41622) covalent geometry : angle 0.63062 (56664) SS BOND : bond 0.00376 ( 51) SS BOND : angle 2.03871 ( 102) hydrogen bonds : bond 0.03860 ( 1482) hydrogen bonds : angle 6.22715 ( 3978) link_BETA1-4 : bond 0.00624 ( 15) link_BETA1-4 : angle 0.81922 ( 45) link_NAG-ASN : bond 0.00349 ( 15) link_NAG-ASN : angle 1.43657 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 143 time to evaluate : 1.638 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: H 9 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5430 (p90) REVERT: H 11 SER cc_start: -0.0111 (OUTLIER) cc_final: -0.0731 (m) REVERT: L 43 LYS cc_start: 0.7091 (pttm) cc_final: 0.6530 (pptt) REVERT: A 185 ASN cc_start: 0.7069 (t0) cc_final: 0.6750 (t0) REVERT: T 103 MET cc_start: 0.1505 (ptp) cc_final: 0.0981 (ptp) REVERT: K 92 TYR cc_start: 0.8486 (t80) cc_final: 0.8278 (t80) REVERT: B 211 ASN cc_start: 0.7468 (t0) cc_final: 0.7166 (t0) REVERT: B 1029 MET cc_start: 0.8697 (tpp) cc_final: 0.8382 (ttp) REVERT: W 65 PHE cc_start: 0.5752 (m-80) cc_final: 0.5505 (m-80) REVERT: W 71 MET cc_start: 0.8369 (mtm) cc_final: 0.7607 (mmm) REVERT: W 82 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.5049 (mtp) REVERT: S 32 ASN cc_start: 0.7487 (m110) cc_final: 0.7076 (t0) REVERT: X 61 TYR cc_start: 0.8311 (m-10) cc_final: 0.7917 (m-80) REVERT: X 71 MET cc_start: 0.8393 (tpt) cc_final: 0.8132 (mmt) REVERT: P 39 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8194 (mpt90) REVERT: C 562 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.2949 (m-10) outliers start: 98 outliers final: 80 residues processed: 228 average time/residue: 0.2348 time to fit residues: 92.3469 Evaluate side-chains 223 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 139 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 82 MET Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 GLN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 480 optimal weight: 0.9990 chunk 29 optimal weight: 50.0000 chunk 87 optimal weight: 5.9990 chunk 516 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 501 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 233 optimal weight: 40.0000 chunk 22 optimal weight: 50.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 955 ASN M 74 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.093209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.062307 restraints weight = 276975.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.063309 restraints weight = 138301.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.063148 restraints weight = 95635.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.063177 restraints weight = 63637.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.063125 restraints weight = 63256.151| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 41703 Z= 0.255 Angle : 0.681 12.957 56856 Z= 0.347 Chirality : 0.045 0.228 6462 Planarity : 0.005 0.065 7278 Dihedral : 5.565 48.807 6280 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.08 % Allowed : 17.56 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -2.34 (0.11), residues: 5196 helix: 0.94 (0.19), residues: 714 sheet: -1.60 (0.13), residues: 1500 loop : -2.22 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 567 TYR 0.029 0.001 TYR I 53 PHE 0.034 0.002 PHE C 306 TRP 0.016 0.001 TRP W 37 HIS 0.008 0.001 HIS P 36 Details of bonding type rmsd covalent geometry : bond 0.00560 (41622) covalent geometry : angle 0.67419 (56664) SS BOND : bond 0.00439 ( 51) SS BOND : angle 2.08645 ( 102) hydrogen bonds : bond 0.04083 ( 1482) hydrogen bonds : angle 6.33810 ( 3978) link_BETA1-4 : bond 0.00502 ( 15) link_BETA1-4 : angle 1.03065 ( 45) link_NAG-ASN : bond 0.00797 ( 15) link_NAG-ASN : angle 1.74786 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 141 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5825 (OUTLIER) cc_final: 0.4968 (p90) REVERT: H 11 SER cc_start: -0.0111 (OUTLIER) cc_final: -0.0797 (m) REVERT: L 43 LYS cc_start: 0.6921 (pttm) cc_final: 0.6545 (pptt) REVERT: A 185 ASN cc_start: 0.6796 (t0) cc_final: 0.6529 (t0) REVERT: T 103 MET cc_start: 0.1266 (ptp) cc_final: 0.0809 (ptp) REVERT: I 103 MET cc_start: 0.4509 (ttt) cc_final: 0.3870 (tmm) REVERT: K 92 TYR cc_start: 0.8484 (t80) cc_final: 0.8242 (t80) REVERT: B 1029 MET cc_start: 0.8756 (tpp) cc_final: 0.8432 (ttp) REVERT: W 71 MET cc_start: 0.8192 (mtm) cc_final: 0.6552 (mmm) REVERT: W 82 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4871 (mtp) REVERT: S 32 ASN cc_start: 0.7465 (m110) cc_final: 0.7088 (t0) REVERT: X 61 TYR cc_start: 0.8268 (m-10) cc_final: 0.7862 (m-10) REVERT: X 71 MET cc_start: 0.8218 (tpt) cc_final: 0.7897 (mmt) REVERT: X 109 PHE cc_start: 0.8441 (m-10) cc_final: 0.8201 (m-10) REVERT: C 562 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.3242 (m-10) outliers start: 91 outliers final: 77 residues processed: 217 average time/residue: 0.2298 time to fit residues: 86.4343 Evaluate side-chains 214 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 133 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 50 TYR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 82 MET Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 GLN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 342 optimal weight: 0.0270 chunk 414 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 327 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 447 optimal weight: 50.0000 chunk 344 optimal weight: 3.9990 chunk 504 optimal weight: 1.9990 chunk 198 optimal weight: 50.0000 chunk 296 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1108 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.093976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.064423 restraints weight = 279156.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064562 restraints weight = 159451.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.064807 restraints weight = 109920.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.064517 restraints weight = 96027.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.064589 restraints weight = 87780.940| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41703 Z= 0.143 Angle : 0.615 13.150 56856 Z= 0.315 Chirality : 0.044 0.190 6462 Planarity : 0.004 0.066 7278 Dihedral : 5.330 57.988 6279 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.85 % Allowed : 17.88 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.12 (0.11), residues: 5196 helix: 1.36 (0.20), residues: 675 sheet: -1.49 (0.13), residues: 1527 loop : -2.08 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 567 TYR 0.025 0.001 TYR C 904 PHE 0.035 0.001 PHE C 306 TRP 0.016 0.001 TRP W 37 HIS 0.008 0.001 HIS P 36 Details of bonding type rmsd covalent geometry : bond 0.00313 (41622) covalent geometry : angle 0.60995 (56664) SS BOND : bond 0.00314 ( 51) SS BOND : angle 1.71439 ( 102) hydrogen bonds : bond 0.03721 ( 1482) hydrogen bonds : angle 5.99963 ( 3978) link_BETA1-4 : bond 0.00584 ( 15) link_BETA1-4 : angle 0.83330 ( 45) link_NAG-ASN : bond 0.00279 ( 15) link_NAG-ASN : angle 1.23903 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10676.46 seconds wall clock time: 184 minutes 29.28 seconds (11069.28 seconds total)