Starting phenix.real_space_refine on Fri Mar 6 08:40:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbv_24989/03_2026/7sbv_24989.map" } resolution = 3.1 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= 0.004 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 188 5.16 5 C 18624 2.51 5 N 4776 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29339 Number of models: 1 Model: "" Number of chains: 24 Chain: "J" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9145 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 5 Chain: "A" Number of atoms: 9115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9115 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 53, 'TRANS': 1118} Chain breaks: 7 Chain: "B" Number of atoms: 9199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9199 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 53, 'TRANS': 1129} Chain breaks: 6 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: "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: "U" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'8Z9': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Unusual residues: {'8Z9': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.28, per 1000 atoms: 0.25 Number of scatterers: 29339 At special positions: 0 Unit cell: (150.38, 149.35, 193.64, 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 188 16.00 O 5751 8.00 N 4776 7.00 C 18624 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.02 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.03 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.03 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=2.18 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.05 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.02 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.06 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.07 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.07 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.02 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.02 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.07 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.05 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.08 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.04 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.06 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.04 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.02 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.01 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.11 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.02 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.08 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.04 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 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 449 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A 675 " " NAG A1407 " - " ASN A 695 " " NAG A1408 " - " ASN A 648 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 449 " " NAG B1403 " - " ASN B 787 " " NAG B1404 " - " ASN B 936 " " NAG B1405 " - " ASN B 675 " " NAG B1406 " - " ASN B 648 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 738 " " NAG E 1 " - " ASN J1193 " " NAG F 1 " - " ASN J 206 " " NAG G 1 " - " ASN A 137 " " NAG I 1 " - " ASN A 371 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 371 " " NAG J1403 " - " ASN J 449 " " NAG J1404 " - " ASN J 713 " " NAG J1405 " - " ASN J 787 " " NAG J1406 " - " ASN J 936 " " NAG J1407 " - " ASN J 675 " " NAG J1408 " - " ASN J 695 " " NAG J1409 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A1193 " " NAG N 1 " - " ASN A 206 " " NAG O 1 " - " ASN B 137 " " NAG P 1 " - " ASN B 371 " " NAG Q 1 " - " ASN B 713 " " NAG R 1 " - " ASN B 738 " " NAG S 1 " - " ASN B1193 " " NAG T 1 " - " ASN B 206 " " NAG U 1 " - " ASN B 695 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 78 sheets defined 25.4% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'J' and resid 93 through 96 removed outlier: 3.721A pdb=" N LYS J 96 " --> pdb=" O LEU J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 96' Processing helix chain 'J' and resid 263 through 267 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 removed outlier: 3.707A pdb=" N TRP J 360 " --> pdb=" O PRO J 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 357 through 360' Processing helix chain 'J' and resid 371 through 379 removed outlier: 5.061A pdb=" N SER J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 418 removed outlier: 3.658A pdb=" N GLN J 418 " --> pdb=" O VAL J 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 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 464 removed outlier: 3.945A pdb=" N LYS J 462 " --> pdb=" O SER J 458 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE J 464 " --> pdb=" O TRP J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'J' and resid 474 through 478 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: 4.381A pdb=" N GLN J 839 " --> pdb=" O ALA J 835 " (cutoff:3.500A) Processing helix chain 'J' and resid 844 through 874 removed outlier: 3.910A pdb=" N ASP J 848 " --> pdb=" O GLY J 844 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN J 849 " --> pdb=" O SER J 845 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 853 " --> pdb=" O ASN J 849 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 884 Processing helix chain 'J' and resid 913 through 921 removed outlier: 3.908A pdb=" N LEU J 919 " --> pdb=" O ILE J 915 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 931 Processing helix chain 'J' and resid 932 through 937 removed outlier: 4.470A pdb=" N ASN J 935 " --> pdb=" O ALA J 932 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS J 937 " --> pdb=" O TYR J 934 " (cutoff:3.500A) Processing helix chain 'J' and resid 945 through 952 Processing helix chain 'J' and resid 963 through 977 removed outlier: 3.761A pdb=" N THR J 975 " --> pdb=" O THR J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 992 through 995 Processing helix chain 'J' and resid 996 through 1001 Processing helix chain 'J' and resid 1005 through 1012 removed outlier: 3.987A pdb=" N GLN J1011 " --> pdb=" O ASP J1007 " (cutoff:3.500A) Processing helix chain 'J' and resid 1012 through 1027 Processing helix chain 'J' and resid 1035 through 1051 Processing helix chain 'J' and resid 1052 through 1054 No H-bonds generated for 'chain 'J' and resid 1052 through 1054' Processing helix chain 'J' and resid 1056 through 1061 Processing helix chain 'J' and resid 1069 through 1077 Processing helix chain 'J' and resid 1078 through 1125 removed outlier: 4.852A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG J1088 " --> pdb=" O ALA J1084 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J1089 " --> pdb=" O GLN J1085 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG J1093 " --> pdb=" O LEU J1089 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA J1096 " --> pdb=" O GLY J1092 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN J1103 " --> pdb=" O ALA J1099 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR J1109 " --> pdb=" O LEU J1105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU J1110 " --> pdb=" O SER J1106 " (cutoff:3.500A) Processing helix chain 'J' and resid 1210 through 1212 No H-bonds generated for 'chain 'J' and resid 1210 through 1212' Processing helix chain 'A' and resid 93 through 96 removed outlier: 3.888A pdb=" N LYS A 96 " --> pdb=" O LEU A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 371 through 379 removed outlier: 5.115A 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 removed outlier: 3.789A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 removed outlier: 3.525A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 removed outlier: 5.767A pdb=" N SER A 845 " --> pdb=" O GLU A 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 845' Processing helix chain 'A' and resid 846 through 874 removed outlier: 3.624A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 866 " --> pdb=" O ASP A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 913 through 922 removed outlier: 4.254A pdb=" N LYS A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 977 removed outlier: 3.650A pdb=" N ALA A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1010 Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 5.738A pdb=" N LYS A1014 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1029 Processing helix chain 'A' and resid 1035 through 1057 removed outlier: 3.548A pdb=" N VAL A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1124 removed outlier: 4.825A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.868A 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 263 through 267 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 357 through 360 removed outlier: 3.708A pdb=" N TRP B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 423 through 428 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 461 through 465 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 712 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 843 through 874 removed outlier: 4.022A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.246A 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: 3.782A pdb=" N LEU B 972 " --> pdb=" O SER B 968 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 979 " --> pdb=" O THR B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1001 removed outlier: 3.842A pdb=" N ARG B 998 " --> pdb=" O ASN B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1011 removed outlier: 4.916A pdb=" N SER B1010 " --> pdb=" O ASP B1007 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN B1011 " --> pdb=" O VAL B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1040 through 1057 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 1126 removed outlier: 3.607A pdb=" N ARG B1088 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1126 " --> pdb=" O VAL B1122 " (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 helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'L' and resid 53 through 57 removed outlier: 3.725A pdb=" N UNK L 56 " --> pdb=" O UNK L 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.637A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 65 through 73 removed outlier: 4.320A pdb=" N GLY J 106 " --> pdb=" O LEU J 277 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE J 242 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 80 through 81 removed outlier: 3.534A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 85 through 86 removed outlier: 6.656A pdb=" N THR J 178 " --> pdb=" O THR J 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 101 through 102 removed outlier: 3.792A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 114 through 118 Processing sheet with id=AA8, first strand: chain 'J' and resid 318 through 321 Processing sheet with id=AA9, first strand: chain 'J' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'J' and resid 331 through 335 removed outlier: 4.009A pdb=" N ALA J 331 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 353 through 355 Processing sheet with id=AB3, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.641A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.641A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 398 through 399 Processing sheet with id=AB6, first strand: chain 'J' and resid 484 through 488 Processing sheet with id=AB7, first strand: chain 'J' and resid 491 through 493 removed outlier: 4.443A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'J' and resid 565 through 566 Processing sheet with id=AC1, first strand: chain 'J' and resid 743 through 744 removed outlier: 6.409A pdb=" N TYR J 755 " --> pdb=" O VAL J 751 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU J 749 " --> pdb=" O VAL J 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 784 through 786 removed outlier: 6.269A pdb=" N ASN J 784 " --> pdb=" O LEU B 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 797 through 802 removed outlier: 7.121A pdb=" N LYS J1169 " --> pdb=" O ASN J1191 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN J1191 " --> pdb=" O LYS J1169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 805 through 808 Processing sheet with id=AC5, first strand: chain 'J' and resid 805 through 808 removed outlier: 3.502A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.117A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 877 through 879 Processing sheet with id=AC8, first strand: chain 'J' and resid 889 through 890 Processing sheet with id=AC9, first strand: chain 'J' and resid 1214 through 1216 Processing sheet with id=AD1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AD2, first strand: chain 'A' and resid 40 through 44 removed outlier: 4.254A pdb=" N ILE A 40 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 42 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 79 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 106 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 227 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 229 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 65 through 73 removed outlier: 3.794A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.378A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 680 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.443A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.646A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AD8, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.725A pdb=" N SER A 728 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AE2, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.008A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.008A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AE5, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AE6, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AE7, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AE8, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AE9, first strand: chain 'A' and resid 737 through 744 removed outlier: 6.538A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 797 through 802 Processing sheet with id=AF2, first strand: chain 'A' and resid 805 through 815 removed outlier: 4.028A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.227A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 958 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AF5, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AF6, first strand: chain 'A' and resid 1214 through 1216 Processing sheet with id=AF7, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id=AF8, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.011A pdb=" N SER B 29 " --> pdb=" O LEU B 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.593A pdb=" N ALA B 43 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.782A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 85 through 86 removed outlier: 6.405A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.061A pdb=" N LEU B 163 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B 206 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 165 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS B 204 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 167 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AG5, first strand: chain 'B' and resid 318 through 326 removed outlier: 4.771A pdb=" N VAL B 688 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 324 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 686 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG B 687 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ARG B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.721A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.605A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.605A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AH1, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AH2, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AH3, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AH4, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AH5, first strand: chain 'B' and resid 737 through 744 removed outlier: 6.464A pdb=" N TYR B 737 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ASN B 777 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N SER B 739 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 797 through 802 Processing sheet with id=AH7, first strand: chain 'B' and resid 805 through 815 removed outlier: 4.025A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR B1160 " --> pdb=" O HIS B1141 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS B1141 " --> pdb=" O TYR B1160 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.349A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AI1, first strand: chain 'B' and resid 1214 through 1217 Processing sheet with id=AI2, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.462A pdb=" N GLY B1200 " --> pdb=" O TYR B1205 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR B1205 " --> pdb=" O GLY B1200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.504A pdb=" N UNK H 21 " --> pdb=" O UNK H 8 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.865A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N UNK H 41 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N UNK H 49 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N UNK H 37 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N UNK H 51 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N UNK H 35 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N UNK H 34 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK H 95 " --> pdb=" O UNK H 108 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N UNK H 108 " --> pdb=" O UNK H 95 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AI6, first strand: chain 'L' and resid 43 through 44 1152 hydrogen bonds defined for protein. 3057 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: 8.48 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8642 1.33 - 1.48: 9474 1.48 - 1.62: 11602 1.62 - 1.77: 79 1.77 - 1.91: 174 Bond restraints: 29971 Sorted by residual: bond pdb=" CB HIS J1157 " pdb=" CG HIS J1157 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.11e+01 bond pdb=" CB HIS A 193 " pdb=" CG HIS A 193 " ideal model delta sigma weight residual 1.497 1.399 0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.666 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" CB HIS B 219 " pdb=" CG HIS B 219 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" CB HIS J 483 " pdb=" CG HIS J 483 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.14e+01 ... (remaining 29966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 37071 2.90 - 5.80: 3344 5.80 - 8.70: 361 8.70 - 11.59: 32 11.59 - 14.49: 7 Bond angle restraints: 40815 Sorted by residual: angle pdb=" N PHE J 240 " pdb=" CA PHE J 240 " pdb=" C PHE J 240 " ideal model delta sigma weight residual 111.33 124.77 -13.44 1.21e+00 6.83e-01 1.23e+02 angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.03 129.12 -9.09 9.90e-01 1.02e+00 8.43e+01 angle pdb=" N GLY J1092 " pdb=" CA GLY J1092 " pdb=" C GLY J1092 " ideal model delta sigma weight residual 112.66 98.17 14.49 1.62e+00 3.81e-01 8.00e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 128.73 -8.70 9.90e-01 1.02e+00 7.71e+01 angle pdb=" C ALA J1227 " pdb=" N PRO J1228 " pdb=" CA PRO J1228 " ideal model delta sigma weight residual 119.56 128.49 -8.93 1.02e+00 9.61e-01 7.66e+01 ... (remaining 40810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 18196 25.39 - 50.78: 298 50.78 - 76.16: 65 76.16 - 101.55: 22 101.55 - 126.94: 4 Dihedral angle restraints: 18585 sinusoidal: 7647 harmonic: 10938 Sorted by residual: 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 -86.00 -165.87 79.87 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS J 491 " pdb=" SG CYS J 491 " pdb=" SG CYS J 561 " pdb=" CB CYS J 561 " ideal model delta sinusoidal sigma weight residual -86.00 -129.87 43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -126.46 40.46 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 18582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3349 0.102 - 0.204: 1055 0.204 - 0.306: 249 0.306 - 0.408: 87 0.408 - 0.510: 56 Chirality restraints: 4796 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 4793 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 137 " 0.064 2.00e-02 2.50e+03 6.74e-02 5.68e+01 pdb=" CG ASN A 137 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 137 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 137 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 695 " 0.062 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" CG ASN J 695 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN J 695 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN J 695 " -0.102 2.00e-02 2.50e+03 pdb=" C1 NAG J1408 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 695 " -0.059 2.00e-02 2.50e+03 6.18e-02 4.78e+01 pdb=" CG ASN A 695 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 695 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 695 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.074 2.00e-02 2.50e+03 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7880 2.80 - 3.33: 26677 3.33 - 3.85: 47803 3.85 - 4.38: 59601 4.38 - 4.90: 96316 Nonbonded interactions: 238277 Sorted by model distance: nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.276 2.496 nonbonded pdb=" N LEU J1055 " pdb=" O LEU J1055 " model vdw 2.304 2.496 nonbonded pdb=" N GLY J1092 " pdb=" O GLY J1092 " model vdw 2.305 2.496 nonbonded pdb=" O ASN J 787 " pdb=" OD1 ASP J 788 " model vdw 2.310 3.040 nonbonded pdb=" N ALA A 933 " pdb=" O ALA A 933 " model vdw 2.390 2.496 ... (remaining 238272 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 32 or resid 39 through 900 or resid 910 through \ 1232 or resid 1402 through 1406)) selection = (chain 'B' and (resid 15 through 22 or resid 28 through 32 or resid 39 through 1 \ 51 or resid 160 through 195 or resid 199 through 505 or resid 517 through 760 or \ resid 771 through 900 or resid 910 through 1232 or resid 1402 through 1406)) selection = (chain 'J' and (resid 15 through 22 or resid 28 through 195 or resid 199 through \ 505 or resid 517 through 770 or resid 772 through 1405)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.560 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 31.310 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.023 0.151 30090 Z= 1.215 Angle : 1.777 14.492 41109 Z= 1.178 Chirality : 0.121 0.510 4796 Planarity : 0.009 0.044 5208 Dihedral : 10.305 126.940 11382 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.23 % Allowed : 0.46 % Favored : 99.32 % Cbeta Deviations : 0.14 % 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: -0.22 (0.13), residues: 3489 helix: -1.77 (0.15), residues: 791 sheet: 1.07 (0.17), residues: 755 loop : 0.21 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 454 TYR 0.060 0.008 TYR A 79 PHE 0.038 0.006 PHE A 384 TRP 0.046 0.007 TRP J 460 HIS 0.013 0.002 HIS J1157 Details of bonding type rmsd covalent geometry : bond 0.02271 (29971) covalent geometry : angle 1.76256 (40815) SS BOND : bond 0.02669 ( 63) SS BOND : angle 2.88390 ( 126) hydrogen bonds : bond 0.17529 ( 1109) hydrogen bonds : angle 8.04933 ( 3057) link_BETA1-4 : bond 0.07018 ( 17) link_BETA1-4 : angle 4.85169 ( 51) link_NAG-ASN : bond 0.07729 ( 39) link_NAG-ASN : angle 2.46862 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 311 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 372 MET cc_start: 0.8984 (mmm) cc_final: 0.8770 (mmp) REVERT: A 148 THR cc_start: 0.9112 (m) cc_final: 0.8876 (p) REVERT: B 679 MET cc_start: 0.9039 (mmm) cc_final: 0.8683 (mmt) REVERT: B 992 TYR cc_start: 0.6783 (t80) cc_final: 0.6073 (t80) outliers start: 7 outliers final: 5 residues processed: 317 average time/residue: 0.1993 time to fit residues: 100.6826 Evaluate side-chains 151 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 193 HIS 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: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 426 GLN J 483 HIS J 839 GLN J1061 ASN A 31 ASN A 177 HIS A 252 HIS A 418 GLN A 839 GLN A 849 ASN A 996 GLN A1054 ASN A1213 ASN B 177 HIS B 219 HIS B 426 GLN B 593 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 ASN B1138 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.059795 restraints weight = 67429.648| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.68 r_work: 0.2670 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30090 Z= 0.153 Angle : 0.658 9.810 41109 Z= 0.352 Chirality : 0.045 0.189 4796 Planarity : 0.004 0.053 5208 Dihedral : 7.642 117.785 5242 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.81 % Allowed : 2.73 % Favored : 96.45 % 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: 0.14 (0.14), residues: 3489 helix: -0.06 (0.19), residues: 775 sheet: 0.82 (0.18), residues: 729 loop : -0.02 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 264 TYR 0.020 0.002 TYR J 221 PHE 0.025 0.002 PHE A 218 TRP 0.011 0.001 TRP J 460 HIS 0.007 0.001 HIS J 219 Details of bonding type rmsd covalent geometry : bond 0.00323 (29971) covalent geometry : angle 0.63990 (40815) SS BOND : bond 0.00316 ( 63) SS BOND : angle 0.97871 ( 126) hydrogen bonds : bond 0.05346 ( 1109) hydrogen bonds : angle 5.82725 ( 3057) link_BETA1-4 : bond 0.00222 ( 17) link_BETA1-4 : angle 2.57738 ( 51) link_NAG-ASN : bond 0.00836 ( 39) link_NAG-ASN : angle 2.36080 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 53 THR cc_start: 0.9592 (m) cc_final: 0.9389 (p) REVERT: J 1078 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: A 117 PHE cc_start: 0.8430 (m-80) cc_final: 0.8195 (m-80) REVERT: A 148 THR cc_start: 0.9376 (m) cc_final: 0.8989 (p) REVERT: A 234 THR cc_start: 0.9415 (p) cc_final: 0.9187 (t) REVERT: B 82 MET cc_start: 0.9437 (mmm) cc_final: 0.9103 (mmm) REVERT: B 172 MET cc_start: 0.9337 (mmm) cc_final: 0.9105 (tpp) REVERT: B 943 ILE cc_start: 0.8660 (mm) cc_final: 0.8131 (tp) REVERT: B 1197 MET cc_start: 0.9409 (mtp) cc_final: 0.9186 (mtp) outliers start: 25 outliers final: 17 residues processed: 204 average time/residue: 0.1603 time to fit residues: 55.5559 Evaluate side-chains 141 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 610 SER Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1213 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1194 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 266 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 196 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 301 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 252 HIS J 444 ASN J1058 GLN J1071 GLN A 641 GLN A 849 ASN A 996 GLN A1054 ASN B 252 HIS B 996 GLN B1061 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.057563 restraints weight = 67511.603| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.66 r_work: 0.2621 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30090 Z= 0.157 Angle : 0.585 8.781 41109 Z= 0.312 Chirality : 0.044 0.247 4796 Planarity : 0.004 0.044 5208 Dihedral : 6.712 100.995 5240 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 3.12 % Favored : 95.57 % 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: 3489 helix: 0.46 (0.20), residues: 774 sheet: 0.77 (0.18), residues: 735 loop : -0.24 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 264 TYR 0.016 0.001 TYR B 667 PHE 0.025 0.001 PHE J 218 TRP 0.009 0.001 TRP J 360 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00358 (29971) covalent geometry : angle 0.56997 (40815) SS BOND : bond 0.00345 ( 63) SS BOND : angle 0.92285 ( 126) hydrogen bonds : bond 0.04616 ( 1109) hydrogen bonds : angle 5.33816 ( 3057) link_BETA1-4 : bond 0.00475 ( 17) link_BETA1-4 : angle 2.05178 ( 51) link_NAG-ASN : bond 0.00367 ( 39) link_NAG-ASN : angle 2.00523 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1078 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8475 (m-30) REVERT: J 1217 MET cc_start: 0.9099 (mtm) cc_final: 0.8740 (mpp) REVERT: A 148 THR cc_start: 0.9351 (m) cc_final: 0.8905 (p) REVERT: A 234 THR cc_start: 0.9406 (p) cc_final: 0.9194 (t) REVERT: B 943 ILE cc_start: 0.8663 (mm) cc_final: 0.8198 (tp) REVERT: B 1197 MET cc_start: 0.9353 (mtp) cc_final: 0.9048 (mtp) outliers start: 40 outliers final: 23 residues processed: 170 average time/residue: 0.1669 time to fit residues: 48.2388 Evaluate side-chains 148 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1194 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 271 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 chunk 369 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 533 ASN J 874 ASN J1103 GLN A1054 ASN B 849 ASN B 996 GLN B1138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.053643 restraints weight = 66878.334| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.67 r_work: 0.2520 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 30090 Z= 0.288 Angle : 0.682 9.749 41109 Z= 0.356 Chirality : 0.048 0.279 4796 Planarity : 0.005 0.057 5208 Dihedral : 6.684 77.028 5238 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.53 % Allowed : 3.74 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3489 helix: 0.45 (0.19), residues: 797 sheet: 0.56 (0.18), residues: 719 loop : -0.56 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1093 TYR 0.023 0.002 TYR A 934 PHE 0.030 0.002 PHE A 218 TRP 0.010 0.002 TRP B 348 HIS 0.014 0.002 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00684 (29971) covalent geometry : angle 0.66748 (40815) SS BOND : bond 0.00383 ( 63) SS BOND : angle 1.12245 ( 126) hydrogen bonds : bond 0.05316 ( 1109) hydrogen bonds : angle 5.43856 ( 3057) link_BETA1-4 : bond 0.00432 ( 17) link_BETA1-4 : angle 1.96807 ( 51) link_NAG-ASN : bond 0.00557 ( 39) link_NAG-ASN : angle 2.18688 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1078 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8513 (m-30) REVERT: J 1217 MET cc_start: 0.9228 (mtm) cc_final: 0.8976 (mpp) REVERT: A 89 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8327 (tttt) REVERT: A 148 THR cc_start: 0.9435 (m) cc_final: 0.9022 (p) REVERT: A 1015 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 1135 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8184 (p90) REVERT: B 943 ILE cc_start: 0.8683 (mm) cc_final: 0.8311 (tp) REVERT: B 1197 MET cc_start: 0.9406 (mtp) cc_final: 0.9109 (mtp) outliers start: 47 outliers final: 34 residues processed: 166 average time/residue: 0.1748 time to fit residues: 48.7616 Evaluate side-chains 148 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 610 SER Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1135 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 366 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 305 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 160 GLN J1138 ASN A 606 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.055568 restraints weight = 66941.692| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.68 r_work: 0.2575 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30090 Z= 0.125 Angle : 0.538 8.301 41109 Z= 0.284 Chirality : 0.043 0.223 4796 Planarity : 0.004 0.049 5208 Dihedral : 6.077 78.552 5238 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.30 % Allowed : 4.75 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3489 helix: 0.73 (0.20), residues: 799 sheet: 0.67 (0.18), residues: 714 loop : -0.52 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 264 TYR 0.015 0.001 TYR A 221 PHE 0.018 0.001 PHE A 218 TRP 0.014 0.001 TRP B 192 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00278 (29971) covalent geometry : angle 0.52706 (40815) SS BOND : bond 0.00199 ( 63) SS BOND : angle 0.66882 ( 126) hydrogen bonds : bond 0.04149 ( 1109) hydrogen bonds : angle 5.08866 ( 3057) link_BETA1-4 : bond 0.00454 ( 17) link_BETA1-4 : angle 1.56842 ( 51) link_NAG-ASN : bond 0.00476 ( 39) link_NAG-ASN : angle 1.82989 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1078 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 148 THR cc_start: 0.9419 (m) cc_final: 0.8970 (p) REVERT: A 1015 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 1078 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: B 737 TYR cc_start: 0.7973 (m-80) cc_final: 0.7593 (m-80) REVERT: B 943 ILE cc_start: 0.8605 (mm) cc_final: 0.8207 (tp) REVERT: B 1197 MET cc_start: 0.9355 (mtp) cc_final: 0.9042 (mtp) outliers start: 40 outliers final: 30 residues processed: 159 average time/residue: 0.1664 time to fit residues: 44.7225 Evaluate side-chains 150 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 460 TRP Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1034 THR Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Chi-restraints excluded: chain B residue 1194 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 116 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 chunk 332 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN B1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.056569 restraints weight = 66715.673| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.67 r_work: 0.2603 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30090 Z= 0.105 Angle : 0.506 8.068 41109 Z= 0.268 Chirality : 0.042 0.299 4796 Planarity : 0.004 0.050 5208 Dihedral : 5.653 82.569 5238 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.37 % Allowed : 5.21 % Favored : 93.42 % 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: 3489 helix: 0.97 (0.20), residues: 797 sheet: 0.61 (0.18), residues: 715 loop : -0.46 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 264 TYR 0.013 0.001 TYR J 221 PHE 0.016 0.001 PHE A 218 TRP 0.013 0.001 TRP B 192 HIS 0.006 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00231 (29971) covalent geometry : angle 0.49538 (40815) SS BOND : bond 0.00183 ( 63) SS BOND : angle 0.62507 ( 126) hydrogen bonds : bond 0.03752 ( 1109) hydrogen bonds : angle 4.87298 ( 3057) link_BETA1-4 : bond 0.00430 ( 17) link_BETA1-4 : angle 1.48586 ( 51) link_NAG-ASN : bond 0.00443 ( 39) link_NAG-ASN : angle 1.75570 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1078 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: A 148 THR cc_start: 0.9433 (m) cc_final: 0.8984 (p) REVERT: A 397 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9033 (ttm) REVERT: A 1015 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8521 (tp) REVERT: A 1078 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: B 737 TYR cc_start: 0.8014 (m-80) cc_final: 0.7709 (m-80) REVERT: B 943 ILE cc_start: 0.8605 (mm) cc_final: 0.8238 (tp) REVERT: B 1197 MET cc_start: 0.9334 (mtp) cc_final: 0.9018 (mtp) outliers start: 42 outliers final: 29 residues processed: 156 average time/residue: 0.1671 time to fit residues: 44.3020 Evaluate side-chains 148 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1135 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 275 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A1057 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.070087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.052565 restraints weight = 67633.141| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.68 r_work: 0.2498 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2367 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 30090 Z= 0.358 Angle : 0.694 12.325 41109 Z= 0.359 Chirality : 0.049 0.260 4796 Planarity : 0.005 0.056 5208 Dihedral : 6.396 81.320 5238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.53 % Allowed : 5.34 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.14), residues: 3489 helix: 0.71 (0.19), residues: 801 sheet: 0.50 (0.18), residues: 719 loop : -0.70 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 264 TYR 0.024 0.002 TYR A 633 PHE 0.029 0.002 PHE A 218 TRP 0.010 0.002 TRP B 192 HIS 0.007 0.002 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00848 (29971) covalent geometry : angle 0.67960 (40815) SS BOND : bond 0.00436 ( 63) SS BOND : angle 1.19462 ( 126) hydrogen bonds : bond 0.05311 ( 1109) hydrogen bonds : angle 5.31872 ( 3057) link_BETA1-4 : bond 0.00484 ( 17) link_BETA1-4 : angle 1.77784 ( 51) link_NAG-ASN : bond 0.00677 ( 39) link_NAG-ASN : angle 2.28014 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 303 MET cc_start: 0.9195 (tpt) cc_final: 0.8777 (tpt) REVERT: J 1078 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: A 148 THR cc_start: 0.9469 (m) cc_final: 0.9033 (p) REVERT: A 397 MET cc_start: 0.9319 (ttm) cc_final: 0.9099 (ttm) REVERT: A 1015 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 1078 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: B 737 TYR cc_start: 0.8059 (m-80) cc_final: 0.7725 (m-80) REVERT: B 943 ILE cc_start: 0.8692 (mm) cc_final: 0.8340 (tp) REVERT: B 1176 ILE cc_start: 0.8627 (tp) cc_final: 0.8426 (tp) REVERT: B 1197 MET cc_start: 0.9430 (mtp) cc_final: 0.9170 (mtp) outliers start: 47 outliers final: 34 residues processed: 157 average time/residue: 0.1765 time to fit residues: 46.8122 Evaluate side-chains 152 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 460 TRP Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Chi-restraints excluded: chain B residue 1192 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 341 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 307 optimal weight: 0.9980 chunk 325 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 282 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 225 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 606 HIS ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.055957 restraints weight = 66635.303| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.69 r_work: 0.2578 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30090 Z= 0.107 Angle : 0.526 9.631 41109 Z= 0.278 Chirality : 0.042 0.235 4796 Planarity : 0.004 0.053 5208 Dihedral : 5.802 86.073 5238 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.24 % Allowed : 5.60 % Favored : 93.16 % 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: -0.01 (0.14), residues: 3489 helix: 0.99 (0.20), residues: 800 sheet: 0.55 (0.18), residues: 719 loop : -0.62 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 264 TYR 0.015 0.001 TYR A 221 PHE 0.016 0.001 PHE A 218 TRP 0.017 0.001 TRP B 192 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00229 (29971) covalent geometry : angle 0.51570 (40815) SS BOND : bond 0.00187 ( 63) SS BOND : angle 0.85421 ( 126) hydrogen bonds : bond 0.03908 ( 1109) hydrogen bonds : angle 4.96936 ( 3057) link_BETA1-4 : bond 0.00438 ( 17) link_BETA1-4 : angle 1.36714 ( 51) link_NAG-ASN : bond 0.00491 ( 39) link_NAG-ASN : angle 1.73075 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 125 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8187 (mp0) REVERT: J 1078 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: A 89 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8709 (tttt) REVERT: A 148 THR cc_start: 0.9450 (m) cc_final: 0.9011 (p) REVERT: A 397 MET cc_start: 0.9338 (ttm) cc_final: 0.9021 (ttm) REVERT: A 1015 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 1078 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: B 737 TYR cc_start: 0.7950 (m-80) cc_final: 0.7652 (m-80) REVERT: B 943 ILE cc_start: 0.8658 (mm) cc_final: 0.8269 (tp) REVERT: B 1197 MET cc_start: 0.9360 (mtp) cc_final: 0.9051 (mtp) outliers start: 38 outliers final: 29 residues processed: 150 average time/residue: 0.1738 time to fit residues: 44.6765 Evaluate side-chains 149 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1135 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 274 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 318 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 353 optimal weight: 30.0000 chunk 164 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.055301 restraints weight = 66747.168| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.67 r_work: 0.2558 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30090 Z= 0.154 Angle : 0.542 8.704 41109 Z= 0.285 Chirality : 0.043 0.269 4796 Planarity : 0.004 0.059 5208 Dihedral : 5.760 89.153 5238 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.07 % Allowed : 5.92 % Favored : 93.00 % 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: 0.03 (0.14), residues: 3489 helix: 1.08 (0.20), residues: 799 sheet: 0.60 (0.18), residues: 706 loop : -0.63 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 264 TYR 0.014 0.001 TYR J 221 PHE 0.020 0.001 PHE A 218 TRP 0.013 0.001 TRP B 192 HIS 0.007 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00361 (29971) covalent geometry : angle 0.53049 (40815) SS BOND : bond 0.00228 ( 63) SS BOND : angle 0.91828 ( 126) hydrogen bonds : bond 0.04156 ( 1109) hydrogen bonds : angle 4.95507 ( 3057) link_BETA1-4 : bond 0.00393 ( 17) link_BETA1-4 : angle 1.46178 ( 51) link_NAG-ASN : bond 0.00398 ( 39) link_NAG-ASN : angle 1.82588 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 125 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8226 (mp0) REVERT: J 303 MET cc_start: 0.9082 (tpt) cc_final: 0.8628 (tpt) REVERT: J 1078 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 89 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8773 (tttt) REVERT: A 148 THR cc_start: 0.9455 (m) cc_final: 0.9026 (p) REVERT: A 191 LEU cc_start: 0.9034 (tp) cc_final: 0.8809 (tp) REVERT: A 397 MET cc_start: 0.9347 (ttm) cc_final: 0.9021 (ttm) REVERT: A 1015 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 1078 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 737 TYR cc_start: 0.7974 (m-80) cc_final: 0.7669 (m-80) REVERT: B 943 ILE cc_start: 0.8663 (mm) cc_final: 0.8283 (tp) REVERT: B 1197 MET cc_start: 0.9391 (mtp) cc_final: 0.9085 (mtp) outliers start: 33 outliers final: 25 residues processed: 140 average time/residue: 0.1713 time to fit residues: 40.9978 Evaluate side-chains 144 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 274 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 349 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.056230 restraints weight = 66348.906| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.67 r_work: 0.2586 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30090 Z= 0.122 Angle : 0.513 8.127 41109 Z= 0.271 Chirality : 0.042 0.260 4796 Planarity : 0.004 0.055 5208 Dihedral : 5.543 84.860 5238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.07 % Allowed : 5.96 % Favored : 92.97 % 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: 0.07 (0.14), residues: 3489 helix: 1.16 (0.20), residues: 799 sheet: 0.59 (0.18), residues: 710 loop : -0.61 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 264 TYR 0.014 0.001 TYR J 221 PHE 0.020 0.001 PHE A1135 TRP 0.015 0.001 TRP B 192 HIS 0.008 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00279 (29971) covalent geometry : angle 0.50220 (40815) SS BOND : bond 0.00175 ( 63) SS BOND : angle 0.82367 ( 126) hydrogen bonds : bond 0.03842 ( 1109) hydrogen bonds : angle 4.86154 ( 3057) link_BETA1-4 : bond 0.00415 ( 17) link_BETA1-4 : angle 1.34742 ( 51) link_NAG-ASN : bond 0.00395 ( 39) link_NAG-ASN : angle 1.70948 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 125 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8226 (mp0) REVERT: J 1078 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: A 89 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8748 (tttt) REVERT: A 148 THR cc_start: 0.9442 (m) cc_final: 0.9005 (p) REVERT: A 191 LEU cc_start: 0.9029 (tp) cc_final: 0.8782 (tp) REVERT: A 397 MET cc_start: 0.9360 (ttm) cc_final: 0.9062 (ttm) REVERT: A 1015 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 1078 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: B 737 TYR cc_start: 0.7978 (m-80) cc_final: 0.7680 (m-80) REVERT: B 943 ILE cc_start: 0.8622 (mm) cc_final: 0.8255 (tp) REVERT: B 1197 MET cc_start: 0.9354 (mtp) cc_final: 0.9031 (mtp) outliers start: 33 outliers final: 24 residues processed: 139 average time/residue: 0.1786 time to fit residues: 42.5384 Evaluate side-chains 141 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 218 PHE Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 775 PHE Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 756 CYS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1078 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 156 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 185 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.056402 restraints weight = 67042.212| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.70 r_work: 0.2585 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30090 Z= 0.115 Angle : 0.510 7.975 41109 Z= 0.270 Chirality : 0.042 0.261 4796 Planarity : 0.004 0.051 5208 Dihedral : 5.424 78.503 5238 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.94 % Allowed : 6.09 % Favored : 92.97 % 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: 0.13 (0.14), residues: 3489 helix: 1.28 (0.20), residues: 792 sheet: 0.62 (0.18), residues: 707 loop : -0.59 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.013 0.001 TYR J 221 PHE 0.022 0.001 PHE A1135 TRP 0.014 0.001 TRP B 192 HIS 0.008 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00262 (29971) covalent geometry : angle 0.49889 (40815) SS BOND : bond 0.00173 ( 63) SS BOND : angle 0.80455 ( 126) hydrogen bonds : bond 0.03799 ( 1109) hydrogen bonds : angle 4.82393 ( 3057) link_BETA1-4 : bond 0.00398 ( 17) link_BETA1-4 : angle 1.34919 ( 51) link_NAG-ASN : bond 0.00437 ( 39) link_NAG-ASN : angle 1.73668 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6435.62 seconds wall clock time: 111 minutes 20.11 seconds (6680.11 seconds total)