Starting phenix.real_space_refine on Fri Mar 6 09:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.map" model { file = "/net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sby_24992/03_2026/7sby_24992.cif" } resolution = 3.0 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= 0.009 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 189 5.16 5 C 18618 2.51 5 N 4767 2.21 5 O 5740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s 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: 29314 Number of models: 1 Model: "" Number of chains: 23 Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "J" Number of atoms: 9114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9114 Classifications: {'peptide': 1171} Link IDs: {'PTRANS': 52, 'TRANS': 1118} Chain breaks: 7 Chain: "A" Number of atoms: 9147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9147 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9097 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 50, 'TRANS': 1118} Chain breaks: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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: "S" 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: "T" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'8Z9': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'8Z9': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.02, per 1000 atoms: 0.24 Number of scatterers: 29314 At special positions: 0 Unit cell: (152.44, 148.32, 181.28, 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 189 16.00 O 5740 8.00 N 4767 7.00 C 18618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.02 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.02 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.03 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.07 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.03 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.09 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.16 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.05 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.07 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.09 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.01 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.11 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.11 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.01 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.05 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.01 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.04 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.13 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.06 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.08 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.06 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.07 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.13 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.07 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.10 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.09 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1401 " - " ASN A 449 " " NAG A1402 " - " ASN A 675 " " NAG A1403 " - " ASN A 648 " " NAG A1404 " - " ASN A 695 " " NAG A1405 " - " ASN A 787 " " NAG A1406 " - " ASN A1223 " " NAG B1401 " - " ASN B 936 " " NAG B1402 " - " ASN B 63 " " NAG B1403 " - " ASN B 212 " " NAG B1404 " - " ASN B 449 " " NAG B1405 " - " ASN B 648 " " NAG B1406 " - " ASN B 713 " " NAG B1407 " - " ASN B 787 " " NAG B1408 " - " ASN B1193 " " NAG B1409 " - " ASN B1223 " " NAG C 1 " - " ASN J 371 " " NAG D 1 " - " ASN J 206 " " NAG E 1 " - " ASN J 675 " " NAG F 1 " - " ASN A 206 " " NAG G 1 " - " ASN A 371 " " NAG I 1 " - " ASN A 713 " " NAG J1401 " - " ASN J 137 " " NAG J1402 " - " ASN J 212 " " NAG J1403 " - " ASN J 449 " " NAG J1404 " - " ASN J 713 " " NAG J1405 " - " ASN J 738 " " NAG J1406 " - " ASN J 787 " " NAG J1407 " - " ASN J 936 " " NAG J1408 " - " ASN J1193 " " NAG J1409 " - " ASN J 695 " " NAG J1410 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A1193 " " NAG N 1 " - " ASN A 936 " " NAG O 1 " - " ASN A 137 " " NAG P 1 " - " ASN B 738 " " NAG Q 1 " - " ASN B 137 " " NAG R 1 " - " ASN B 206 " " NAG S 1 " - " ASN B 371 " " NAG T 1 " - " ASN B 675 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7010 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 81 sheets defined 26.1% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'J' and resid 93 through 96 Processing helix chain 'J' and resid 181 through 185 Processing helix chain 'J' and resid 301 through 310 Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 360 Processing helix chain 'J' and resid 371 through 376 Processing helix chain 'J' and resid 390 through 394 Processing helix chain 'J' and resid 413 through 418 Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 448 through 450 No H-bonds generated for 'chain 'J' and resid 448 through 450' Processing helix chain 'J' and resid 458 through 463 Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'J' and resid 538 through 542 Processing helix chain 'J' and resid 707 through 712 Processing helix chain 'J' and resid 824 through 830 Processing helix chain 'J' and resid 833 through 841 removed outlier: 3.692A pdb=" N VAL J 841 " --> pdb=" O LYS J 837 " (cutoff:3.500A) Processing helix chain 'J' and resid 843 through 874 removed outlier: 3.939A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 884 Processing helix chain 'J' and resid 913 through 922 removed outlier: 4.259A pdb=" N LYS J 922 " --> pdb=" O LEU J 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 935 Processing helix chain 'J' and resid 945 through 952 Processing helix chain 'J' and resid 963 through 980 removed outlier: 3.560A pdb=" N THR J 975 " --> pdb=" O THR J 971 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 990 through 1001 Processing helix chain 'J' and resid 1008 through 1011 Processing helix chain 'J' and resid 1012 through 1029 Processing helix chain 'J' and resid 1035 through 1057 removed outlier: 3.698A pdb=" N GLN J1057 " --> pdb=" O ASN J1053 " (cutoff:3.500A) Processing helix chain 'J' and resid 1058 through 1061 Processing helix chain 'J' and resid 1069 through 1077 Processing helix chain 'J' and resid 1078 through 1125 removed outlier: 4.748A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR J1109 " --> pdb=" O LEU J1105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU J1110 " --> pdb=" O SER J1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.733A pdb=" N TRP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.963A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 removed outlier: 3.904A pdb=" N GLN A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 874 removed outlier: 3.917A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 913 through 922 removed outlier: 4.280A pdb=" N LYS A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 935 Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 977 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1035 through 1058 removed outlier: 4.052A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1061 No H-bonds generated for 'chain 'A' and resid 1059 through 1061' Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 4.812A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 357 through 360 Processing helix chain 'B' and resid 371 through 379 removed outlier: 4.248A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.828A pdb=" N LYS B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 841 removed outlier: 4.330A pdb=" N GLN B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 874 removed outlier: 4.070A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.374A pdb=" N LYS B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 935 Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 963 through 980 removed outlier: 4.276A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 979 " --> pdb=" O THR B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 999 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1035 through 1057 removed outlier: 4.083A pdb=" N ALA B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B1048 " --> pdb=" O VAL B1044 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B1053 " --> pdb=" O ALA B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1061 Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1098 removed outlier: 3.879A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1125 removed outlier: 3.687A pdb=" N THR B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1110 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.616A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 103 through 104 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 53 through 54 removed outlier: 6.733A pdb=" N UNK L 53 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK L 84 " --> pdb=" O UNK L 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.733A pdb=" N UNK L 53 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK L 84 " --> pdb=" O UNK L 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 29 through 31 Processing sheet with id=AA8, first strand: chain 'J' and resid 42 through 44 removed outlier: 8.303A pdb=" N THR J 78 " --> pdb=" O PRO J 276 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 64 through 72 removed outlier: 3.799A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 114 through 118 Processing sheet with id=AB2, first strand: chain 'J' and resid 204 through 209 removed outlier: 3.675A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 191 through 193 removed outlier: 7.818A pdb=" N HIS J 193 " --> pdb=" O TYR J 175 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N TYR J 175 " --> pdb=" O HIS J 193 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR J 259 " --> pdb=" O PRO J 176 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR J 178 " --> pdb=" O THR J 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 318 through 321 Processing sheet with id=AB5, first strand: chain 'J' and resid 325 through 326 Processing sheet with id=AB6, first strand: chain 'J' and resid 332 through 335 removed outlier: 4.201A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE J 669 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN J 657 " --> pdb=" O PHE J 669 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 58 " --> pdb=" O GLN J 656 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 353 through 355 Processing sheet with id=AB8, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.612A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.612A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 369 through 370 Processing sheet with id=AC2, first strand: chain 'J' and resid 484 through 488 Processing sheet with id=AC3, first strand: chain 'J' and resid 492 through 493 Processing sheet with id=AC4, first strand: chain 'J' and resid 498 through 502 removed outlier: 3.764A pdb=" N CYS J 499 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU J 529 " --> pdb=" O CYS J 499 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS J 501 " --> pdb=" O LEU J 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 520 through 521 Processing sheet with id=AC6, first strand: chain 'J' and resid 565 through 566 Processing sheet with id=AC7, first strand: chain 'J' and resid 737 through 744 removed outlier: 6.444A pdb=" N TYR J 737 " --> pdb=" O PHE J 775 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASN J 777 " --> pdb=" O TYR J 737 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N SER J 739 " --> pdb=" O ASN J 777 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR J 755 " --> pdb=" O VAL J 751 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 784 through 786 removed outlier: 6.140A pdb=" N ASN J 784 " --> pdb=" O LEU B 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 797 through 802 Processing sheet with id=AD1, first strand: chain 'J' and resid 805 through 815 removed outlier: 4.029A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR J1160 " --> pdb=" O HIS J1141 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N HIS J1141 " --> pdb=" O TYR J1160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.212A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 877 through 879 Processing sheet with id=AD4, first strand: chain 'J' and resid 889 through 890 Processing sheet with id=AD5, first strand: chain 'J' and resid 1214 through 1217 removed outlier: 5.950A pdb=" N CYS J1175 " --> pdb=" O ALA J1227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id=AD7, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'A' and resid 42 through 44 removed outlier: 8.252A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 227 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 229 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.808A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 65 through 72 removed outlier: 3.560A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 85 through 86 removed outlier: 8.259A pdb=" N THR A 259 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N TYR A 175 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS A 193 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.880A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AE5, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AE6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.036A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.741A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 361 through 366 removed outlier: 6.590A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AF2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AF3, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AF4, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AF5, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AF6, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AF7, first strand: chain 'A' and resid 737 through 744 removed outlier: 6.564A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 797 through 815 removed outlier: 6.895A pdb=" N GLU A 798 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A1169 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 800 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1167 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A1165 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A 804 " --> pdb=" O THR A1163 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.161A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AG2, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AG3, first strand: chain 'A' and resid 1214 through 1216 Processing sheet with id=AG4, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 4.710A pdb=" N GLY A1200 " --> pdb=" O TYR A1205 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR A1205 " --> pdb=" O GLY A1200 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AG6, first strand: chain 'B' and resid 42 through 44 removed outlier: 8.403A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.607A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 85 through 86 removed outlier: 8.304A pdb=" N THR B 259 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N TYR B 175 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS B 193 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 101 through 102 removed outlier: 4.232A pdb=" N ALA B 128 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AH2, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AH3, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AH4, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.781A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.670A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.670A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AH8, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AH9, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AI1, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AI2, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AI3, first strand: chain 'B' and resid 737 through 744 removed outlier: 6.548A pdb=" N TYR B 737 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASN B 777 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N SER B 739 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 797 through 802 Processing sheet with id=AI5, first strand: chain 'B' and resid 805 through 815 removed outlier: 4.061A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B1160 " --> pdb=" O HIS B1141 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS B1141 " --> pdb=" O TYR B1160 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.162A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AI8, first strand: chain 'B' and resid 1214 through 1217 removed outlier: 5.882A pdb=" N CYS B1175 " --> pdb=" O ALA B1227 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'B' and resid 1187 through 1192 1239 hydrogen bonds defined for protein. 3273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.97 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 8615 1.33 - 1.48: 9653 1.48 - 1.63: 11427 1.63 - 1.78: 86 1.78 - 1.93: 160 Bond restraints: 29941 Sorted by residual: bond pdb=" CB TYR J 725 " pdb=" CG TYR J 725 " ideal model delta sigma weight residual 1.512 1.373 0.139 2.20e-02 2.07e+03 3.98e+01 bond pdb=" CB ASN J 171 " pdb=" CG ASN J 171 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.95e+01 bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.421 0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" CB HIS B 219 " pdb=" CG HIS B 219 " ideal model delta sigma weight residual 1.497 1.422 0.075 1.40e-02 5.10e+03 2.84e+01 bond pdb=" CG GLN A 426 " pdb=" CD GLN A 426 " ideal model delta sigma weight residual 1.516 1.384 0.132 2.50e-02 1.60e+03 2.77e+01 ... (remaining 29936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 40753 10.31 - 20.63: 13 20.63 - 30.94: 0 30.94 - 41.26: 4 41.26 - 51.57: 2 Bond angle restraints: 40772 Sorted by residual: angle pdb=" C8 NAG B1404 " pdb=" C7 NAG B1404 " pdb=" N2 NAG B1404 " ideal model delta sigma weight residual 115.06 166.63 -51.57 3.00e+00 1.11e-01 2.96e+02 angle pdb=" N2 NAG B1404 " pdb=" C7 NAG B1404 " pdb=" O7 NAG B1404 " ideal model delta sigma weight residual 123.46 79.77 43.69 3.00e+00 1.11e-01 2.12e+02 angle pdb=" C2 NAG T 1 " pdb=" N2 NAG T 1 " pdb=" C7 NAG T 1 " ideal model delta sigma weight residual 124.56 162.02 -37.46 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C2 NAG M 2 " pdb=" N2 NAG M 2 " pdb=" C7 NAG M 2 " ideal model delta sigma weight residual 124.56 160.97 -36.41 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG J1407 " pdb=" N2 NAG J1407 " pdb=" C7 NAG J1407 " ideal model delta sigma weight residual 124.56 160.36 -35.80 3.00e+00 1.11e-01 1.42e+02 ... (remaining 40767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.09: 18259 29.09 - 58.17: 237 58.17 - 87.26: 62 87.26 - 116.34: 11 116.34 - 145.43: 2 Dihedral angle restraints: 18571 sinusoidal: 7640 harmonic: 10931 Sorted by residual: dihedral pdb=" CB CYS A 535 " pdb=" SG CYS A 535 " pdb=" SG CYS A 548 " pdb=" CB CYS A 548 " ideal model delta sinusoidal sigma weight residual -86.00 -161.16 75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS J 535 " pdb=" SG CYS J 535 " pdb=" SG CYS J 548 " pdb=" CB CYS J 548 " ideal model delta sinusoidal sigma weight residual 93.00 132.93 -39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 368 " pdb=" CB CYS A 368 " ideal model delta sinusoidal sigma weight residual 93.00 53.32 39.68 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 18568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3453 0.108 - 0.217: 1010 0.217 - 0.325: 218 0.325 - 0.434: 84 0.434 - 0.542: 37 Chirality restraints: 4802 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.97e+01 ... (remaining 4799 not shown) Planarity restraints: 5235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 212 " -0.069 2.00e-02 2.50e+03 7.34e-02 6.74e+01 pdb=" CG ASN J 212 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN J 212 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN J 212 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG J1402 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 675 " 0.057 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" CG ASN B 675 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 675 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 675 " -0.095 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 713 " -0.054 2.00e-02 2.50e+03 5.74e-02 4.12e+01 pdb=" CG ASN J 713 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN J 713 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN J 713 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG J1404 " -0.070 2.00e-02 2.50e+03 ... (remaining 5232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6016 2.77 - 3.30: 26168 3.30 - 3.84: 47365 3.84 - 4.37: 59950 4.37 - 4.90: 98506 Nonbonded interactions: 238005 Sorted by model distance: nonbonded pdb=" N TRP A 94 " pdb=" O TRP A 94 " model vdw 2.238 2.496 nonbonded pdb=" N TRP B 94 " pdb=" O TRP B 94 " model vdw 2.285 2.496 nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.298 2.496 nonbonded pdb=" N ASN B1046 " pdb=" O ASN B1046 " model vdw 2.323 2.496 nonbonded pdb=" N VAL B 136 " pdb=" O VAL B 136 " model vdw 2.367 2.496 ... (remaining 238000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 23 or resid 28 through 194 or resid 199 through \ 474 or resid 478 through 760 or resid 771 through 901 or resid 911 through 1232 \ or resid 1401 through 1406)) selection = (chain 'B' and (resid 15 through 23 or resid 28 through 194 or resid 199 through \ 760 or resid 771 through 901 or resid 911 through 1232 or resid 1402 through 14 \ 07)) selection = (chain 'J' and (resid 15 through 23 or resid 28 through 32 or resid 39 through 4 \ 74 or resid 478 through 760 or resid 771 through 901 or resid 911 through 1232 o \ r resid 1402 through 1407)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.380 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.022 0.139 30061 Z= 1.121 Angle : 1.805 51.570 41069 Z= 1.161 Chirality : 0.121 0.542 4802 Planarity : 0.008 0.034 5195 Dihedral : 10.881 145.426 11372 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.16 % Allowed : 0.39 % Favored : 99.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3472 helix: -1.04 (0.15), residues: 811 sheet: 0.90 (0.17), residues: 785 loop : 0.40 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 998 TYR 0.057 0.008 TYR A 79 PHE 0.028 0.005 PHE J 464 TRP 0.040 0.007 TRP A 655 HIS 0.006 0.002 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.02150 (29941) covalent geometry : angle 1.78972 (40772) SS BOND : bond 0.03548 ( 63) SS BOND : angle 3.13526 ( 126) hydrogen bonds : bond 0.16793 ( 1192) hydrogen bonds : angle 7.43637 ( 3273) link_BETA1-4 : bond 0.07202 ( 17) link_BETA1-4 : angle 4.63523 ( 51) link_NAG-ASN : bond 0.07599 ( 40) link_NAG-ASN : angle 2.64297 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 582 time to evaluate : 1.044 Fit side-chains REVERT: J 20 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6524 (tptt) REVERT: J 118 LYS cc_start: 0.5822 (tttt) cc_final: 0.5535 (ttmp) REVERT: J 234 THR cc_start: 0.8152 (p) cc_final: 0.7574 (t) REVERT: J 303 MET cc_start: 0.8656 (tpt) cc_final: 0.8375 (tpt) REVERT: J 372 MET cc_start: 0.8745 (mmm) cc_final: 0.8137 (mmm) REVERT: J 581 GLN cc_start: 0.8224 (pt0) cc_final: 0.7918 (pm20) REVERT: J 698 GLU cc_start: 0.7892 (pt0) cc_final: 0.7527 (pt0) REVERT: J 927 ASP cc_start: 0.7341 (p0) cc_final: 0.7110 (p0) REVERT: J 1081 GLU cc_start: 0.7386 (tp30) cc_final: 0.7171 (tp30) REVERT: J 1197 MET cc_start: 0.8756 (mtp) cc_final: 0.8536 (mtp) REVERT: J 1229 TYR cc_start: 0.7623 (m-80) cc_final: 0.7381 (m-80) REVERT: A 210 ASP cc_start: 0.8339 (t0) cc_final: 0.7736 (t0) REVERT: A 258 LEU cc_start: 0.8505 (tp) cc_final: 0.8303 (tt) REVERT: A 268 PHE cc_start: 0.8413 (t80) cc_final: 0.8180 (t80) REVERT: A 394 ILE cc_start: 0.8714 (pt) cc_final: 0.8250 (mt) REVERT: A 547 LYS cc_start: 0.7499 (tttt) cc_final: 0.7243 (ttpp) REVERT: A 684 TYR cc_start: 0.8393 (t80) cc_final: 0.8087 (t80) REVERT: A 848 ASP cc_start: 0.8470 (m-30) cc_final: 0.8227 (m-30) REVERT: A 873 MET cc_start: 0.8743 (mmm) cc_final: 0.8458 (mmt) REVERT: A 1179 ASP cc_start: 0.7080 (m-30) cc_final: 0.6565 (t0) REVERT: B 122 MET cc_start: 0.8079 (ttp) cc_final: 0.7747 (ttp) REVERT: B 181 HIS cc_start: 0.7254 (t-90) cc_final: 0.7050 (t-90) REVERT: B 259 THR cc_start: 0.8201 (m) cc_final: 0.7958 (p) REVERT: B 268 PHE cc_start: 0.7899 (t80) cc_final: 0.7522 (t80) REVERT: B 698 GLU cc_start: 0.7726 (pt0) cc_final: 0.7389 (pp20) REVERT: B 856 GLU cc_start: 0.7709 (tt0) cc_final: 0.7378 (tm-30) outliers start: 5 outliers final: 1 residues processed: 585 average time/residue: 0.5526 time to fit residues: 386.3624 Evaluate side-chains 273 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 ASN J 187 HIS ** J 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 ASN J1058 GLN J1223 ASN A 31 ASN A 63 ASN A 186 ASN A 252 HIS A 380 GLN A 619 GLN A 663 ASN A 839 GLN A 965 ASN A1028 GLN A1035 ASN A1213 ASN B 219 HIS B 252 HIS B 421 ASN B 469 ASN B 579 GLN B 695 ASN B 784 ASN B1000 ASN B1053 ASN B1098 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.095461 restraints weight = 37850.625| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.86 r_work: 0.2886 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30061 Z= 0.144 Angle : 0.756 43.430 41069 Z= 0.372 Chirality : 0.046 0.382 4802 Planarity : 0.004 0.049 5195 Dihedral : 7.956 134.243 5249 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.75 % Allowed : 7.42 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3472 helix: 0.79 (0.19), residues: 788 sheet: 0.80 (0.17), residues: 806 loop : 0.10 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.023 0.002 TYR A 79 PHE 0.019 0.002 PHE B 67 TRP 0.025 0.002 TRP A 460 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00303 (29941) covalent geometry : angle 0.73874 (40772) SS BOND : bond 0.00411 ( 63) SS BOND : angle 1.22408 ( 126) hydrogen bonds : bond 0.05421 ( 1192) hydrogen bonds : angle 5.59003 ( 3273) link_BETA1-4 : bond 0.00499 ( 17) link_BETA1-4 : angle 2.38800 ( 51) link_NAG-ASN : bond 0.00534 ( 40) link_NAG-ASN : angle 2.52401 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6503 (tppp) REVERT: J 223 GLU cc_start: 0.8389 (tt0) cc_final: 0.8030 (tt0) REVERT: J 234 THR cc_start: 0.7848 (p) cc_final: 0.7302 (t) REVERT: J 303 MET cc_start: 0.8617 (tpt) cc_final: 0.8323 (tpt) REVERT: J 372 MET cc_start: 0.8856 (mmm) cc_final: 0.8214 (mmm) REVERT: J 581 GLN cc_start: 0.8005 (pt0) cc_final: 0.7404 (pm20) REVERT: J 584 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8150 (pt) REVERT: J 1081 GLU cc_start: 0.7666 (tp30) cc_final: 0.7139 (tp30) REVERT: J 1223 ASN cc_start: 0.7568 (m-40) cc_final: 0.7097 (m110) REVERT: J 1229 TYR cc_start: 0.7435 (m-80) cc_final: 0.7102 (m-80) REVERT: A 210 ASP cc_start: 0.7945 (t0) cc_final: 0.7668 (t0) REVERT: A 268 PHE cc_start: 0.8436 (t80) cc_final: 0.8125 (t80) REVERT: A 299 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: A 394 ILE cc_start: 0.8680 (pt) cc_final: 0.8065 (mt) REVERT: A 473 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7597 (tppp) REVERT: A 684 TYR cc_start: 0.8598 (t80) cc_final: 0.8217 (t80) REVERT: A 745 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7324 (mp10) REVERT: A 848 ASP cc_start: 0.8674 (m-30) cc_final: 0.8344 (m-30) REVERT: A 1057 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8533 (tp-100) REVERT: A 1179 ASP cc_start: 0.6925 (m-30) cc_final: 0.6119 (t0) REVERT: B 117 PHE cc_start: 0.6845 (m-80) cc_final: 0.6347 (m-80) REVERT: B 122 MET cc_start: 0.8103 (ttp) cc_final: 0.7844 (ttp) REVERT: B 150 ASN cc_start: 0.5885 (t0) cc_final: 0.5667 (m-40) REVERT: B 181 HIS cc_start: 0.6995 (t-90) cc_final: 0.6716 (t-90) REVERT: B 259 THR cc_start: 0.8107 (m) cc_final: 0.7828 (p) REVERT: B 584 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 698 GLU cc_start: 0.8362 (pt0) cc_final: 0.8158 (pt0) REVERT: B 798 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: B 856 GLU cc_start: 0.8186 (tt0) cc_final: 0.7558 (tm-30) REVERT: B 999 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7899 (mt) REVERT: B 1210 THR cc_start: 0.8824 (t) cc_final: 0.8614 (p) outliers start: 84 outliers final: 27 residues processed: 388 average time/residue: 0.5022 time to fit residues: 236.2187 Evaluate side-chains 292 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 171 ASN Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 595 ASP Chi-restraints excluded: chain J residue 682 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 946 LEU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1213 ASN Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 223 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 359 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 219 HIS J 421 ASN J 444 ASN J 735 ASN A 32 ASN A 63 ASN A 219 HIS A 483 HIS A 497 ASN A 532 HIS A1138 ASN B 160 GLN B 171 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.090119 restraints weight = 38002.851| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.79 r_work: 0.2789 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30061 Z= 0.264 Angle : 0.841 43.992 41069 Z= 0.412 Chirality : 0.051 0.292 4802 Planarity : 0.005 0.053 5195 Dihedral : 7.658 115.720 5249 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.79 % Allowed : 8.30 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3472 helix: 0.88 (0.19), residues: 797 sheet: 0.48 (0.17), residues: 810 loop : -0.37 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 413 TYR 0.027 0.002 TYR J 79 PHE 0.023 0.002 PHE B 67 TRP 0.014 0.002 TRP A 460 HIS 0.013 0.002 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00639 (29941) covalent geometry : angle 0.82570 (40772) SS BOND : bond 0.00575 ( 63) SS BOND : angle 1.64654 ( 126) hydrogen bonds : bond 0.06056 ( 1192) hydrogen bonds : angle 5.47973 ( 3273) link_BETA1-4 : bond 0.00760 ( 17) link_BETA1-4 : angle 2.20440 ( 51) link_NAG-ASN : bond 0.00479 ( 40) link_NAG-ASN : angle 2.33694 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 272 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.7101 (mmtt) cc_final: 0.6446 (tptt) REVERT: J 199 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7581 (p) REVERT: J 372 MET cc_start: 0.9012 (mmm) cc_final: 0.8474 (mmm) REVERT: J 387 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7394 (p0) REVERT: J 547 LYS cc_start: 0.6766 (mmtt) cc_final: 0.6483 (mtpp) REVERT: J 581 GLN cc_start: 0.8096 (pt0) cc_final: 0.7761 (pm20) REVERT: J 725 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.5921 (t80) REVERT: J 1071 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: J 1081 GLU cc_start: 0.7800 (tp30) cc_final: 0.7352 (tp30) REVERT: J 1180 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6981 (mtp85) REVERT: J 1223 ASN cc_start: 0.7571 (m-40) cc_final: 0.7077 (m110) REVERT: J 1229 TYR cc_start: 0.7431 (m-80) cc_final: 0.7125 (m-80) REVERT: A 234 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7929 (t) REVERT: A 268 PHE cc_start: 0.8486 (t80) cc_final: 0.8096 (t80) REVERT: A 394 ILE cc_start: 0.8755 (pt) cc_final: 0.8180 (mt) REVERT: A 502 LYS cc_start: 0.6328 (mtmt) cc_final: 0.5905 (mtpp) REVERT: A 745 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7377 (mp-120) REVERT: A 848 ASP cc_start: 0.8659 (m-30) cc_final: 0.8334 (m-30) REVERT: A 888 PHE cc_start: 0.6644 (p90) cc_final: 0.6428 (p90) REVERT: A 890 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 1057 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8702 (tp40) REVERT: A 1179 ASP cc_start: 0.7012 (m-30) cc_final: 0.6262 (t0) REVERT: B 89 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7638 (ttmt) REVERT: B 117 PHE cc_start: 0.7127 (m-80) cc_final: 0.6685 (m-80) REVERT: B 122 MET cc_start: 0.8114 (ttp) cc_final: 0.7842 (ttp) REVERT: B 181 HIS cc_start: 0.7010 (t-90) cc_final: 0.6655 (t-90) REVERT: B 259 THR cc_start: 0.8232 (m) cc_final: 0.7870 (p) REVERT: B 584 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8507 (mt) REVERT: B 748 ASP cc_start: 0.8213 (m-30) cc_final: 0.7738 (m-30) REVERT: B 798 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: B 888 PHE cc_start: 0.7206 (m-80) cc_final: 0.6643 (p90) REVERT: B 1072 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 1081 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7470 (tm-30) outliers start: 116 outliers final: 57 residues processed: 347 average time/residue: 0.4899 time to fit residues: 206.5304 Evaluate side-chains 311 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 243 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 723 ILE Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 758 ASP Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 946 LEU Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1071 GLN Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1180 ARG Chi-restraints excluded: chain J residue 1213 ASN Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 165 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 230 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 304 optimal weight: 0.0270 chunk 331 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 overall best weight: 1.2840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 ASN A 31 ASN A 150 ASN A 482 ASN A 490 HIS A 532 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.091469 restraints weight = 37752.848| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.85 r_work: 0.2844 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30061 Z= 0.117 Angle : 0.687 43.457 41069 Z= 0.327 Chirality : 0.044 0.257 4802 Planarity : 0.004 0.048 5195 Dihedral : 6.600 99.047 5249 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.55 % Allowed : 10.17 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3472 helix: 1.35 (0.19), residues: 794 sheet: 0.57 (0.17), residues: 823 loop : -0.40 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.019 0.001 TYR B 79 PHE 0.015 0.001 PHE B 67 TRP 0.015 0.001 TRP A 460 HIS 0.007 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00254 (29941) covalent geometry : angle 0.67301 (40772) SS BOND : bond 0.00311 ( 63) SS BOND : angle 1.06170 ( 126) hydrogen bonds : bond 0.04434 ( 1192) hydrogen bonds : angle 5.11057 ( 3273) link_BETA1-4 : bond 0.00492 ( 17) link_BETA1-4 : angle 1.78872 ( 51) link_NAG-ASN : bond 0.00429 ( 40) link_NAG-ASN : angle 2.20388 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 271 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6373 (tptt) REVERT: J 372 MET cc_start: 0.8987 (mmm) cc_final: 0.8277 (mmm) REVERT: J 387 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7449 (p0) REVERT: J 581 GLN cc_start: 0.8094 (pt0) cc_final: 0.7830 (pm20) REVERT: J 725 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.5964 (t80) REVERT: J 1066 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (pt) REVERT: J 1081 GLU cc_start: 0.7587 (tp30) cc_final: 0.7056 (tp30) REVERT: J 1223 ASN cc_start: 0.7524 (m-40) cc_final: 0.7090 (m110) REVERT: J 1229 TYR cc_start: 0.7284 (m-80) cc_final: 0.7077 (m-80) REVERT: A 31 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6885 (p0) REVERT: A 268 PHE cc_start: 0.8542 (t80) cc_final: 0.8106 (t80) REVERT: A 394 ILE cc_start: 0.8798 (pt) cc_final: 0.8570 (pp) REVERT: A 468 GLU cc_start: 0.8179 (mp0) cc_final: 0.7967 (mp0) REVERT: A 502 LYS cc_start: 0.6322 (mtmt) cc_final: 0.5859 (mtpp) REVERT: A 745 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7365 (mp-120) REVERT: A 848 ASP cc_start: 0.8550 (m-30) cc_final: 0.8223 (m-30) REVERT: A 888 PHE cc_start: 0.6592 (p90) cc_final: 0.6381 (p90) REVERT: A 1057 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8537 (tp-100) REVERT: A 1179 ASP cc_start: 0.7007 (m-30) cc_final: 0.6263 (t0) REVERT: B 117 PHE cc_start: 0.7173 (m-80) cc_final: 0.6786 (m-80) REVERT: B 125 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: B 181 HIS cc_start: 0.6851 (t-90) cc_final: 0.6495 (t-90) REVERT: B 259 THR cc_start: 0.8150 (m) cc_final: 0.7797 (p) REVERT: B 584 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8337 (mt) REVERT: B 748 ASP cc_start: 0.8164 (m-30) cc_final: 0.7610 (m-30) REVERT: B 888 PHE cc_start: 0.7103 (m-80) cc_final: 0.6648 (p90) REVERT: B 1072 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7622 (mt-10) outliers start: 78 outliers final: 36 residues processed: 315 average time/residue: 0.5072 time to fit residues: 193.7257 Evaluate side-chains 277 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 171 ASN Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 444 ASN Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1213 ASN Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 984 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 80 optimal weight: 0.5980 chunk 224 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 239 optimal weight: 0.0980 chunk 9 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 347 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 735 ASN J1057 GLN ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1103 GLN A 31 ASN A 32 ASN A 150 ASN A 532 HIS B 849 ASN B1213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.090929 restraints weight = 38097.753| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.81 r_work: 0.2831 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30061 Z= 0.131 Angle : 0.683 43.445 41069 Z= 0.326 Chirality : 0.044 0.260 4802 Planarity : 0.004 0.085 5195 Dihedral : 6.245 89.773 5249 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.78 % Allowed : 10.20 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3472 helix: 1.47 (0.19), residues: 793 sheet: 0.55 (0.17), residues: 818 loop : -0.45 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 59 TYR 0.020 0.001 TYR J 79 PHE 0.013 0.001 PHE A 126 TRP 0.013 0.001 TRP A 460 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00298 (29941) covalent geometry : angle 0.67058 (40772) SS BOND : bond 0.00325 ( 63) SS BOND : angle 1.00597 ( 126) hydrogen bonds : bond 0.04463 ( 1192) hydrogen bonds : angle 5.02769 ( 3273) link_BETA1-4 : bond 0.00512 ( 17) link_BETA1-4 : angle 1.69959 ( 51) link_NAG-ASN : bond 0.00401 ( 40) link_NAG-ASN : angle 2.17975 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 252 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.6945 (mmtt) cc_final: 0.6402 (tptt) REVERT: J 194 MET cc_start: 0.7298 (ttt) cc_final: 0.7084 (mmm) REVERT: J 372 MET cc_start: 0.8979 (mmm) cc_final: 0.8282 (mmm) REVERT: J 387 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7408 (p0) REVERT: J 547 LYS cc_start: 0.6777 (mmtt) cc_final: 0.6475 (mtpp) REVERT: J 581 GLN cc_start: 0.8102 (pt0) cc_final: 0.7812 (pm20) REVERT: J 717 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8133 (pp) REVERT: J 725 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6003 (t80) REVERT: J 888 PHE cc_start: 0.7002 (m-80) cc_final: 0.5888 (p90) REVERT: J 1223 ASN cc_start: 0.7523 (m-40) cc_final: 0.7082 (m110) REVERT: A 234 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7967 (t) REVERT: A 268 PHE cc_start: 0.8570 (t80) cc_final: 0.8138 (t80) REVERT: A 394 ILE cc_start: 0.8772 (pt) cc_final: 0.8526 (pp) REVERT: A 502 LYS cc_start: 0.6376 (mtmt) cc_final: 0.5838 (mtpp) REVERT: A 745 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7374 (mp10) REVERT: A 848 ASP cc_start: 0.8526 (m-30) cc_final: 0.8210 (m-30) REVERT: A 1028 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (mm110) REVERT: A 1057 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8651 (tp40) REVERT: A 1179 ASP cc_start: 0.7029 (m-30) cc_final: 0.6267 (t0) REVERT: B 117 PHE cc_start: 0.7243 (m-80) cc_final: 0.6891 (m-80) REVERT: B 125 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: B 181 HIS cc_start: 0.6742 (t-90) cc_final: 0.6389 (t-90) REVERT: B 259 THR cc_start: 0.8145 (m) cc_final: 0.7808 (p) REVERT: B 493 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8542 (ptpt) REVERT: B 584 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 748 ASP cc_start: 0.8183 (m-30) cc_final: 0.7657 (m-30) REVERT: B 761 LYS cc_start: 0.6758 (mptt) cc_final: 0.6546 (mptt) REVERT: B 798 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: B 859 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: B 888 PHE cc_start: 0.7113 (m-80) cc_final: 0.6649 (p90) REVERT: B 1006 MET cc_start: 0.8981 (mmm) cc_final: 0.8624 (mmm) REVERT: B 1072 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 85 outliers final: 53 residues processed: 311 average time/residue: 0.5373 time to fit residues: 201.6291 Evaluate side-chains 299 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 444 ASN Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 758 ASP Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 364 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 444 ASN ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1140 ASN A 150 ASN A 482 ASN B 482 ASN B 532 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.086481 restraints weight = 38778.582| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.68 r_work: 0.2770 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 30061 Z= 0.321 Angle : 0.866 43.709 41069 Z= 0.422 Chirality : 0.053 0.303 4802 Planarity : 0.006 0.082 5195 Dihedral : 7.228 100.505 5249 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.79 % Allowed : 9.64 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3472 helix: 1.00 (0.19), residues: 783 sheet: 0.35 (0.17), residues: 804 loop : -0.83 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 413 TYR 0.031 0.003 TYR J 79 PHE 0.019 0.003 PHE J 286 TRP 0.015 0.002 TRP J 655 HIS 0.038 0.002 HIS A 532 Details of bonding type rmsd covalent geometry : bond 0.00778 (29941) covalent geometry : angle 0.85072 (40772) SS BOND : bond 0.00620 ( 63) SS BOND : angle 1.62250 ( 126) hydrogen bonds : bond 0.06247 ( 1192) hydrogen bonds : angle 5.51592 ( 3273) link_BETA1-4 : bond 0.00682 ( 17) link_BETA1-4 : angle 2.06342 ( 51) link_NAG-ASN : bond 0.00434 ( 40) link_NAG-ASN : angle 2.50464 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 255 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.6999 (mmtt) cc_final: 0.6620 (tptt) REVERT: J 372 MET cc_start: 0.8977 (mmm) cc_final: 0.8261 (mmm) REVERT: J 387 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7505 (p0) REVERT: J 547 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6739 (mtpp) REVERT: J 581 GLN cc_start: 0.8199 (pt0) cc_final: 0.7887 (pm20) REVERT: J 584 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8275 (pt) REVERT: J 717 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8287 (pp) REVERT: J 718 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6535 (mtp180) REVERT: J 725 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6054 (t80) REVERT: J 888 PHE cc_start: 0.7074 (m-80) cc_final: 0.6184 (p90) REVERT: J 1081 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: J 1103 GLN cc_start: 0.8258 (mt0) cc_final: 0.7957 (mt0) REVERT: J 1223 ASN cc_start: 0.7552 (m-40) cc_final: 0.7085 (m110) REVERT: A 115 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8083 (mttm) REVERT: A 234 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8090 (t) REVERT: A 268 PHE cc_start: 0.8518 (t80) cc_final: 0.8267 (t80) REVERT: A 394 ILE cc_start: 0.8772 (pt) cc_final: 0.8530 (pp) REVERT: A 502 LYS cc_start: 0.6416 (mtmt) cc_final: 0.5956 (mtpp) REVERT: A 745 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7400 (mp10) REVERT: A 890 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 1057 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8571 (tp-100) REVERT: A 1179 ASP cc_start: 0.7105 (m-30) cc_final: 0.6386 (t0) REVERT: B 117 PHE cc_start: 0.7421 (m-80) cc_final: 0.6938 (m-80) REVERT: B 125 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: B 181 HIS cc_start: 0.6774 (t-90) cc_final: 0.6398 (t-90) REVERT: B 259 THR cc_start: 0.8308 (m) cc_final: 0.8067 (p) REVERT: B 473 LYS cc_start: 0.6070 (mttp) cc_final: 0.5575 (mmtm) REVERT: B 584 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 748 ASP cc_start: 0.8401 (m-30) cc_final: 0.8022 (m-30) REVERT: B 888 PHE cc_start: 0.7215 (m-80) cc_final: 0.6783 (p90) REVERT: B 946 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7859 (mp) REVERT: B 1006 MET cc_start: 0.8950 (mmm) cc_final: 0.8547 (mmm) outliers start: 116 outliers final: 71 residues processed: 340 average time/residue: 0.5406 time to fit residues: 221.4859 Evaluate side-chains 318 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 234 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 718 ARG Chi-restraints excluded: chain J residue 723 ILE Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 746 THR Chi-restraints excluded: chain J residue 758 ASP Chi-restraints excluded: chain J residue 783 VAL Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1081 GLU Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1213 ASN Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 113 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 324 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 345 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1058 GLN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN A 150 ASN A 532 HIS B 606 HIS B 839 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093059 restraints weight = 38353.381| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.58 r_work: 0.2841 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30061 Z= 0.111 Angle : 0.666 43.370 41069 Z= 0.316 Chirality : 0.043 0.290 4802 Planarity : 0.004 0.070 5195 Dihedral : 6.196 82.109 5249 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 12.00 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3472 helix: 1.44 (0.19), residues: 793 sheet: 0.55 (0.17), residues: 792 loop : -0.72 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 147 TYR 0.020 0.001 TYR J 570 PHE 0.015 0.001 PHE B 980 TRP 0.017 0.001 TRP J 655 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00240 (29941) covalent geometry : angle 0.65533 (40772) SS BOND : bond 0.00383 ( 63) SS BOND : angle 0.82728 ( 126) hydrogen bonds : bond 0.04110 ( 1192) hydrogen bonds : angle 5.02005 ( 3273) link_BETA1-4 : bond 0.00468 ( 17) link_BETA1-4 : angle 1.53337 ( 51) link_NAG-ASN : bond 0.00345 ( 40) link_NAG-ASN : angle 2.08979 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 20 LYS cc_start: 0.6801 (mmtt) cc_final: 0.6320 (tptt) REVERT: J 212 ASN cc_start: 0.7581 (m-40) cc_final: 0.7342 (t0) REVERT: J 372 MET cc_start: 0.8907 (mmm) cc_final: 0.8241 (mmm) REVERT: J 387 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7474 (p0) REVERT: J 581 GLN cc_start: 0.8131 (pt0) cc_final: 0.7861 (pm20) REVERT: J 584 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8283 (pt) REVERT: J 725 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6072 (t80) REVERT: J 888 PHE cc_start: 0.7005 (m-80) cc_final: 0.6127 (p90) REVERT: J 1219 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7666 (p) REVERT: J 1223 ASN cc_start: 0.7465 (m-40) cc_final: 0.7023 (m110) REVERT: A 79 TYR cc_start: 0.8851 (m-80) cc_final: 0.8651 (m-80) REVERT: A 115 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7938 (mttm) REVERT: A 234 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8071 (t) REVERT: A 268 PHE cc_start: 0.8461 (t80) cc_final: 0.8078 (t80) REVERT: A 502 LYS cc_start: 0.6396 (mtmt) cc_final: 0.5937 (mtpp) REVERT: A 584 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8546 (pp) REVERT: A 745 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7339 (mp10) REVERT: A 1057 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8408 (tp-100) REVERT: A 1179 ASP cc_start: 0.7014 (m-30) cc_final: 0.6327 (t0) REVERT: B 117 PHE cc_start: 0.7361 (m-80) cc_final: 0.6968 (m-80) REVERT: B 181 HIS cc_start: 0.6710 (t-90) cc_final: 0.6376 (t-90) REVERT: B 259 THR cc_start: 0.8200 (m) cc_final: 0.7953 (p) REVERT: B 493 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8423 (ptpt) REVERT: B 519 ILE cc_start: 0.7233 (mm) cc_final: 0.6890 (mm) REVERT: B 584 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 748 ASP cc_start: 0.8240 (m-30) cc_final: 0.7807 (m-30) REVERT: B 888 PHE cc_start: 0.7155 (m-80) cc_final: 0.6769 (p90) outliers start: 58 outliers final: 31 residues processed: 292 average time/residue: 0.5192 time to fit residues: 182.2670 Evaluate side-chains 277 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 999 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 293 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 282 optimal weight: 0.7980 chunk 264 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 444 ASN J 724 ASN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.091440 restraints weight = 38553.857| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.63 r_work: 0.2810 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30061 Z= 0.198 Angle : 0.744 43.611 41069 Z= 0.357 Chirality : 0.047 0.259 4802 Planarity : 0.005 0.070 5195 Dihedral : 6.587 87.201 5249 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.42 % Allowed : 11.96 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3472 helix: 1.36 (0.19), residues: 789 sheet: 0.53 (0.18), residues: 778 loop : -0.82 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 80 TYR 0.023 0.002 TYR J 79 PHE 0.016 0.002 PHE J 220 TRP 0.021 0.002 TRP J 655 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00472 (29941) covalent geometry : angle 0.73126 (40772) SS BOND : bond 0.00415 ( 63) SS BOND : angle 1.17931 ( 126) hydrogen bonds : bond 0.05126 ( 1192) hydrogen bonds : angle 5.19315 ( 3273) link_BETA1-4 : bond 0.00534 ( 17) link_BETA1-4 : angle 1.66277 ( 51) link_NAG-ASN : bond 0.00347 ( 40) link_NAG-ASN : angle 2.21151 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 1.000 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: J 20 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6533 (tptt) REVERT: J 125 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: J 147 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7572 (mmt90) REVERT: J 194 MET cc_start: 0.6121 (ppp) cc_final: 0.5830 (ttp) REVERT: J 372 MET cc_start: 0.8945 (mmm) cc_final: 0.8250 (mmm) REVERT: J 387 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7596 (p0) REVERT: J 581 GLN cc_start: 0.8135 (pt0) cc_final: 0.7869 (pm20) REVERT: J 584 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8475 (pt) REVERT: J 717 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8223 (pp) REVERT: J 718 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6630 (mtp180) REVERT: J 725 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6077 (t80) REVERT: J 888 PHE cc_start: 0.7090 (m-80) cc_final: 0.6303 (p90) REVERT: J 1103 GLN cc_start: 0.8111 (mt0) cc_final: 0.7845 (mt0) REVERT: J 1223 ASN cc_start: 0.7371 (m-40) cc_final: 0.6959 (m110) REVERT: A 115 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8070 (mttm) REVERT: A 234 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8127 (t) REVERT: A 268 PHE cc_start: 0.8523 (t80) cc_final: 0.8262 (t80) REVERT: A 502 LYS cc_start: 0.6431 (mtmt) cc_final: 0.6023 (mtpp) REVERT: A 584 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 745 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7424 (mp10) REVERT: A 1179 ASP cc_start: 0.7003 (m-30) cc_final: 0.6373 (t0) REVERT: B 117 PHE cc_start: 0.7441 (m-80) cc_final: 0.7060 (m-80) REVERT: B 181 HIS cc_start: 0.6807 (t-90) cc_final: 0.6500 (t-90) REVERT: B 259 THR cc_start: 0.8327 (m) cc_final: 0.8114 (p) REVERT: B 584 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 593 GLN cc_start: 0.8107 (tt0) cc_final: 0.7827 (tt0) REVERT: B 748 ASP cc_start: 0.8468 (m-30) cc_final: 0.8127 (m-30) REVERT: B 859 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: B 888 PHE cc_start: 0.7225 (m-80) cc_final: 0.6926 (p90) outliers start: 74 outliers final: 45 residues processed: 292 average time/residue: 0.5323 time to fit residues: 187.1583 Evaluate side-chains 290 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 718 ARG Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 758 ASP Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 77 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 619 GLN A 31 ASN A 150 ASN A 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.092397 restraints weight = 38363.869| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.52 r_work: 0.2829 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30061 Z= 0.153 Angle : 0.704 43.459 41069 Z= 0.336 Chirality : 0.045 0.283 4802 Planarity : 0.005 0.067 5195 Dihedral : 6.433 82.310 5249 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 12.32 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3472 helix: 1.45 (0.19), residues: 787 sheet: 0.49 (0.18), residues: 788 loop : -0.84 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 147 TYR 0.025 0.002 TYR J 570 PHE 0.014 0.002 PHE A 126 TRP 0.019 0.001 TRP J 655 HIS 0.009 0.001 HIS A 532 Details of bonding type rmsd covalent geometry : bond 0.00356 (29941) covalent geometry : angle 0.69276 (40772) SS BOND : bond 0.00340 ( 63) SS BOND : angle 0.98285 ( 126) hydrogen bonds : bond 0.04678 ( 1192) hydrogen bonds : angle 5.09848 ( 3273) link_BETA1-4 : bond 0.00474 ( 17) link_BETA1-4 : angle 1.52367 ( 51) link_NAG-ASN : bond 0.00323 ( 40) link_NAG-ASN : angle 2.12942 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 1.102 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: J 20 LYS cc_start: 0.6878 (mmtt) cc_final: 0.6453 (tptt) REVERT: J 194 MET cc_start: 0.6087 (ppp) cc_final: 0.5769 (ttp) REVERT: J 372 MET cc_start: 0.8933 (mmm) cc_final: 0.8245 (mmm) REVERT: J 387 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (p0) REVERT: J 581 GLN cc_start: 0.8116 (pt0) cc_final: 0.7834 (pm20) REVERT: J 584 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8446 (pt) REVERT: J 717 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8185 (pp) REVERT: J 718 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6738 (mtp180) REVERT: J 725 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6137 (t80) REVERT: J 888 PHE cc_start: 0.7057 (m-80) cc_final: 0.6318 (p90) REVERT: J 1103 GLN cc_start: 0.8201 (mt0) cc_final: 0.7946 (mt0) REVERT: J 1219 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7705 (p) REVERT: J 1223 ASN cc_start: 0.7344 (m-40) cc_final: 0.6902 (m110) REVERT: A 115 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8037 (mttm) REVERT: A 234 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 268 PHE cc_start: 0.8514 (t80) cc_final: 0.8238 (t80) REVERT: A 394 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8206 (mt) REVERT: A 584 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8635 (pp) REVERT: A 745 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7420 (mp10) REVERT: A 1179 ASP cc_start: 0.6981 (m-30) cc_final: 0.6386 (t0) REVERT: B 117 PHE cc_start: 0.7447 (m-80) cc_final: 0.7065 (m-80) REVERT: B 125 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 181 HIS cc_start: 0.6799 (t-90) cc_final: 0.6512 (t-90) REVERT: B 259 THR cc_start: 0.8308 (m) cc_final: 0.8095 (p) REVERT: B 263 ARG cc_start: 0.6409 (mmm-85) cc_final: 0.6082 (mmp-170) REVERT: B 493 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8724 (ptpt) REVERT: B 584 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 593 GLN cc_start: 0.8094 (tt0) cc_final: 0.7812 (tt0) REVERT: B 748 ASP cc_start: 0.8436 (m-30) cc_final: 0.8037 (m-30) REVERT: B 761 LYS cc_start: 0.6501 (mptt) cc_final: 0.6269 (tptm) REVERT: B 859 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: B 888 PHE cc_start: 0.7204 (m-80) cc_final: 0.6937 (p90) outliers start: 67 outliers final: 44 residues processed: 282 average time/residue: 0.5275 time to fit residues: 180.6622 Evaluate side-chains 291 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 718 ARG Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1220 CYS Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 2 optimal weight: 20.0000 chunk 364 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 258 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 444 ASN A 150 ASN A 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.089236 restraints weight = 38476.882| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.56 r_work: 0.2780 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30061 Z= 0.214 Angle : 0.767 43.666 41069 Z= 0.369 Chirality : 0.048 0.289 4802 Planarity : 0.005 0.071 5195 Dihedral : 6.718 84.283 5249 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 12.32 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3472 helix: 1.26 (0.19), residues: 789 sheet: 0.42 (0.18), residues: 790 loop : -0.93 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 147 TYR 0.025 0.002 TYR J 79 PHE 0.016 0.002 PHE B 980 TRP 0.019 0.002 TRP J 655 HIS 0.009 0.001 HIS A 532 Details of bonding type rmsd covalent geometry : bond 0.00514 (29941) covalent geometry : angle 0.75455 (40772) SS BOND : bond 0.00444 ( 63) SS BOND : angle 1.23312 ( 126) hydrogen bonds : bond 0.05343 ( 1192) hydrogen bonds : angle 5.28053 ( 3273) link_BETA1-4 : bond 0.00518 ( 17) link_BETA1-4 : angle 1.67743 ( 51) link_NAG-ASN : bond 0.00327 ( 40) link_NAG-ASN : angle 2.27052 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 1.022 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: J 20 LYS cc_start: 0.6774 (mmtt) cc_final: 0.6426 (tptt) REVERT: J 194 MET cc_start: 0.6167 (ppp) cc_final: 0.5854 (ttp) REVERT: J 372 MET cc_start: 0.8953 (mmm) cc_final: 0.8395 (mmm) REVERT: J 387 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7423 (p0) REVERT: J 581 GLN cc_start: 0.8153 (pt0) cc_final: 0.7779 (pm20) REVERT: J 584 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8452 (pt) REVERT: J 717 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8342 (pp) REVERT: J 718 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6849 (mtp180) REVERT: J 725 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6046 (t80) REVERT: J 888 PHE cc_start: 0.6977 (m-80) cc_final: 0.6195 (p90) REVERT: J 1103 GLN cc_start: 0.8175 (mt0) cc_final: 0.7933 (mt0) REVERT: J 1219 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7810 (p) REVERT: J 1223 ASN cc_start: 0.7467 (m-40) cc_final: 0.6984 (m110) REVERT: A 115 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7999 (mttm) REVERT: A 234 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 394 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 502 LYS cc_start: 0.6465 (mtmt) cc_final: 0.6116 (mtpp) REVERT: A 584 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 745 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7352 (mp10) REVERT: A 1179 ASP cc_start: 0.6983 (m-30) cc_final: 0.6248 (t0) REVERT: B 82 MET cc_start: 0.8775 (mmt) cc_final: 0.8552 (mmm) REVERT: B 117 PHE cc_start: 0.7442 (m-80) cc_final: 0.7002 (m-80) REVERT: B 125 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 181 HIS cc_start: 0.6641 (t-90) cc_final: 0.6348 (t-90) REVERT: B 259 THR cc_start: 0.8244 (m) cc_final: 0.8020 (p) REVERT: B 263 ARG cc_start: 0.6302 (mmm-85) cc_final: 0.5973 (mmp-170) REVERT: B 584 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 593 GLN cc_start: 0.8043 (tt0) cc_final: 0.7759 (tt0) REVERT: B 717 ILE cc_start: 0.8374 (pt) cc_final: 0.8088 (OUTLIER) REVERT: B 748 ASP cc_start: 0.8375 (m-30) cc_final: 0.8105 (m-30) REVERT: B 859 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B 888 PHE cc_start: 0.7162 (m-80) cc_final: 0.6745 (p90) outliers start: 68 outliers final: 49 residues processed: 282 average time/residue: 0.5194 time to fit residues: 177.0082 Evaluate side-chains 286 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 535 CYS Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 715 SER Chi-restraints excluded: chain J residue 717 ILE Chi-restraints excluded: chain J residue 718 ARG Chi-restraints excluded: chain J residue 725 TYR Chi-restraints excluded: chain J residue 758 ASP Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 926 SER Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1036 SER Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain J residue 1106 SER Chi-restraints excluded: chain J residue 1182 ILE Chi-restraints excluded: chain J residue 1219 THR Chi-restraints excluded: chain J residue 1225 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 1169 LYS Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 444 ASN A 150 ASN A 532 HIS A 874 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.089964 restraints weight = 38655.285| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.52 r_work: 0.2781 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30061 Z= 0.240 Angle : 0.794 43.581 41069 Z= 0.383 Chirality : 0.049 0.272 4802 Planarity : 0.005 0.075 5195 Dihedral : 6.947 81.725 5249 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.55 % Allowed : 11.93 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3472 helix: 1.16 (0.19), residues: 783 sheet: 0.37 (0.18), residues: 789 loop : -1.05 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.027 0.002 TYR J 79 PHE 0.018 0.002 PHE J 712 TRP 0.018 0.002 TRP J 655 HIS 0.009 0.002 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00579 (29941) covalent geometry : angle 0.78065 (40772) SS BOND : bond 0.00488 ( 63) SS BOND : angle 1.32873 ( 126) hydrogen bonds : bond 0.05554 ( 1192) hydrogen bonds : angle 5.36834 ( 3273) link_BETA1-4 : bond 0.00539 ( 17) link_BETA1-4 : angle 1.74510 ( 51) link_NAG-ASN : bond 0.00326 ( 40) link_NAG-ASN : angle 2.34358 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7980.03 seconds wall clock time: 136 minutes 57.70 seconds (8217.70 seconds total)