Starting phenix.real_space_refine on Fri Mar 6 09:33:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbx_24991/03_2026/7sbx_24991.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 189 5.16 5 C 18780 2.51 5 N 4816 2.21 5 O 5814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 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: 29599 Number of models: 1 Model: "" Number of chains: 27 Chain: "J" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9152 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 6 Chain: "A" Number of atoms: 9204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9204 Classifications: {'peptide': 1184} Link IDs: {'PTRANS': 52, 'TRANS': 1131} Chain breaks: 5 Chain: "B" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9197 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 52, 'TRANS': 1130} Chain breaks: 5 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 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: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "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: "V" 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: "W" 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: "X" 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: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'8Z9': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.21, per 1000 atoms: 0.21 Number of scatterers: 29599 At special positions: 0 Unit cell: (150.38, 149.35, 197.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 189 16.00 O 5814 8.00 N 4816 7.00 C 18780 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=2.04 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.03 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=2.11 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.04 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.08 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.10 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.13 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.09 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.05 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=1.70 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=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.05 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.04 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.12 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=2.09 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.08 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=2.08 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=2.05 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.06 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.04 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.02 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.07 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 G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 713 " " NAG A1403 " - " ASN A 787 " " NAG A1404 " - " ASN A 936 " " NAG A1405 " - " ASN A 695 " " NAG A1406 " - " ASN A 648 " " NAG A1407 " - " ASN A 449 " " NAG A1408 " - " ASN A1223 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 713 " " NAG B1403 " - " ASN B 787 " " NAG B1404 " - " ASN B 695 " " NAG B1405 " - " ASN B 648 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 738 " " NAG F 1 " - " ASN J1193 " " NAG G 1 " - " ASN J 206 " " NAG I 1 " - " ASN A 137 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 449 " " NAG J1403 " - " ASN J 713 " " NAG J1404 " - " ASN J 787 " " NAG J1405 " - " ASN J 936 " " NAG J1406 " - " ASN J 675 " " NAG J1407 " - " ASN J 695 " " NAG J1408 " - " ASN J 648 " " NAG J1409 " - " ASN J 63 " " NAG K 1 " - " ASN A 371 " " NAG M 1 " - " ASN A 738 " " NAG N 1 " - " ASN A1193 " " NAG O 1 " - " ASN A 206 " " NAG P 1 " - " ASN A 675 " " NAG Q 1 " - " ASN B 137 " " NAG R 1 " - " ASN B 371 " " NAG S 1 " - " ASN B 449 " " NAG T 1 " - " ASN B 738 " " NAG U 1 " - " ASN B 936 " " NAG V 1 " - " ASN B1193 " " NAG W 1 " - " ASN B 206 " " NAG X 1 " - " ASN B 675 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7066 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 79 sheets defined 25.6% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... 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 356 through 360 Processing helix chain 'J' and resid 371 through 376 Processing helix chain 'J' and resid 390 through 394 Processing helix chain 'J' and resid 413 through 418 Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 448 through 450 No H-bonds generated for 'chain 'J' and resid 448 through 450' Processing helix chain 'J' and resid 458 through 463 Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'J' and resid 538 through 542 Processing helix chain 'J' and resid 707 through 714 Processing helix chain 'J' and resid 824 through 830 Processing helix chain 'J' and resid 833 through 840 Processing helix chain 'J' and resid 843 through 874 removed outlier: 3.628A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 884 Processing helix chain 'J' and resid 913 through 922 removed outlier: 4.285A pdb=" N LYS J 922 " --> pdb=" O LEU J 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 935 Processing helix chain 'J' and resid 945 through 953 Processing helix chain 'J' and resid 963 through 980 removed outlier: 4.292A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 983 through 987 Processing helix chain 'J' and resid 990 through 1001 Processing helix chain 'J' and resid 1005 through 1011 Processing helix chain 'J' and resid 1012 through 1029 Processing helix chain 'J' and resid 1035 through 1057 removed outlier: 4.095A pdb=" N ALA J1047 " --> pdb=" O ALA J1043 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN J1048 " --> pdb=" O VAL J1044 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU J1050 " --> pdb=" O ASN J1046 " (cutoff:3.500A) Processing helix chain 'J' and resid 1058 through 1061 Processing helix chain 'J' and resid 1069 through 1077 Processing helix chain 'J' and resid 1078 through 1125 removed outlier: 4.781A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (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: 3.793A 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 344 through 350 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 371 through 379 removed outlier: 5.096A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 Processing helix chain 'A' and resid 843 through 874 removed outlier: 3.906A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 913 through 921 Processing helix chain 'A' and resid 926 through 935 Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 977 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1035 through 1058 Processing helix chain 'A' and resid 1059 through 1061 No H-bonds generated for 'chain 'A' and resid 1059 through 1061' Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 4.706A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 removed outlier: 3.921A pdb=" N LYS B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 357 through 360 Processing helix chain 'B' and resid 371 through 379 removed outlier: 4.313A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 843 through 874 Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.261A pdb=" N LYS B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 934 Processing helix chain 'B' and resid 935 through 937 No H-bonds generated for 'chain 'B' and resid 935 through 937' Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 963 through 977 Processing helix chain 'B' and resid 983 through 987 Processing helix chain 'B' and resid 990 through 1001 Processing helix chain 'B' and resid 1005 through 1012 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1035 through 1058 removed outlier: 3.504A pdb=" N GLN B1058 " --> pdb=" O ASN B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1061 No H-bonds generated for 'chain 'B' and resid 1059 through 1061' Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1125 removed outlier: 4.834A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (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 42 through 44 removed outlier: 7.888A pdb=" N THR J 78 " --> pdb=" O PRO J 276 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE J 227 " --> pdb=" O ASN J 243 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN J 243 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA J 229 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.996A pdb=" N ASP J 58 " --> pdb=" O GLN A 656 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN A 657 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A 669 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 72 removed outlier: 3.526A 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: 8.379A pdb=" N THR J 259 " --> pdb=" O PRO J 176 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR J 178 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N TYR J 175 " --> pdb=" O HIS J 193 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N HIS J 193 " --> pdb=" O TYR J 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 101 through 102 removed outlier: 3.989A 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: 4.028A pdb=" N ALA J 331 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE J 669 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN J 657 " --> pdb=" O PHE J 669 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN J 656 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 60 " --> pdb=" O GLN J 656 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU J 658 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'J' and resid 361 through 366 removed outlier: 3.952A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 361 through 366 removed outlier: 3.952A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 369 through 370 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 492 through 493 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 737 through 744 removed outlier: 6.465A pdb=" N TYR J 737 " --> pdb=" O PHE J 775 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASN J 777 " --> pdb=" O TYR J 737 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N SER J 739 " --> pdb=" O ASN J 777 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR J 755 " --> pdb=" O VAL J 751 " (cutoff:3.500A) removed outlier: 4.312A 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: 6.132A 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 815 removed outlier: 6.813A pdb=" N GLU J 798 " --> pdb=" O LYS J1169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS J1169 " --> pdb=" O GLU J 798 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN J 800 " --> pdb=" O THR J1167 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR J1167 " --> pdb=" O GLN J 800 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR J1165 " --> pdb=" O PRO J 802 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU J 804 " --> pdb=" O THR J1163 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR J1160 " --> pdb=" O HIS J1141 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS J1141 " --> pdb=" O TYR J1160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.097A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 877 through 879 Processing sheet with id=AC6, first strand: chain 'J' and resid 889 through 890 Processing sheet with id=AC7, first strand: chain 'J' and resid 1214 through 1217 Processing sheet with id=AC8, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id=AC9, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AD1, first strand: chain 'A' and resid 42 through 44 removed outlier: 7.907A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 106 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 227 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 229 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 64 through 73 removed outlier: 3.576A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.863A pdb=" N ASP A 58 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN B 657 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B 669 " --> pdb=" O ASN B 657 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 85 through 86 removed outlier: 8.419A pdb=" N THR A 259 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N TYR A 175 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS A 193 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.741A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AD7, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AD8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AD9, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AE1, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.455A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 361 through 365 Processing sheet with id=AE3, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AE4, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AE5, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AE6, first strand: chain 'A' and resid 498 through 502 removed outlier: 3.661A pdb=" N CYS A 499 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 529 " --> pdb=" O CYS A 499 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS A 501 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 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: 6.482A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 749 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 797 through 815 removed outlier: 6.841A pdb=" N GLU A 798 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS A1169 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 800 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A1167 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR A1165 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU A 804 " --> pdb=" O THR A1163 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.130A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AF4, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AF5, first strand: chain 'A' and resid 1214 through 1217 Processing sheet with id=AF6, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id=AF7, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AF8, first strand: chain 'B' and resid 42 through 44 removed outlier: 7.896A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.804A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 85 through 86 removed outlier: 8.317A pdb=" N THR B 259 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N TYR B 175 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS B 193 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.850A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AG4, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AG5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AG6, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.833A 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: 6.520A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.035A 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 Processing sheet with id=AG9, first strand: chain 'B' and resid 369 through 370 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 498 through 502 removed outlier: 3.743A pdb=" N CYS B 499 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU B 529 " --> pdb=" O CYS B 499 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 501 " --> pdb=" O LEU B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 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 571 through 572 Processing sheet with id=AH6, first strand: chain 'B' and resid 737 through 744 removed outlier: 6.416A pdb=" N TYR B 737 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASN B 777 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N SER B 739 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 797 through 815 removed outlier: 6.811A pdb=" N GLU B 798 " --> pdb=" O LYS B1169 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS B1169 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN B 800 " --> pdb=" O THR B1167 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B1167 " --> pdb=" O GLN B 800 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1165 " --> pdb=" O PRO B 802 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B 804 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR B1160 " --> pdb=" O HIS B1141 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.136A 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 Processing sheet with id=AI3, first strand: chain 'H' and resid 3 through 8 removed outlier: 5.870A pdb=" N UNK H 16 " --> pdb=" O UNK H 83 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N UNK H 83 " --> pdb=" O UNK H 16 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.372A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N UNK H 52 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N UNK H 32 " --> pdb=" O UNK H 52 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 105 through 108 Processing sheet with id=AI6, first strand: chain 'L' and resid 17 through 20 Processing sheet with id=AI7, first strand: chain 'L' and resid 56 through 57 removed outlier: 6.630A pdb=" N UNK L 56 " --> pdb=" O UNK L 52 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N UNK L 39 " --> pdb=" O UNK L 50 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N UNK L 52 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N UNK L 37 " --> pdb=" O UNK L 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N UNK L 99 " --> pdb=" O UNK L 92 " (cutoff:3.500A) 1264 hydrogen bonds defined for protein. 3384 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: 8.52 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6651 1.32 - 1.45: 9552 1.45 - 1.58: 13779 1.58 - 1.72: 9 1.72 - 1.85: 240 Bond restraints: 30231 Sorted by residual: bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG B1405 " pdb=" O5 NAG B1405 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.83e+01 ... (remaining 30226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 37575 2.86 - 5.73: 3237 5.73 - 8.59: 324 8.59 - 11.45: 28 11.45 - 14.32: 7 Bond angle restraints: 41171 Sorted by residual: angle pdb=" C GLN A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta sigma weight residual 122.18 113.95 8.23 6.90e-01 2.10e+00 1.42e+02 angle pdb=" N PRO J 981 " pdb=" CA PRO J 981 " pdb=" C PRO J 981 " ideal model delta sigma weight residual 110.70 122.70 -12.00 1.22e+00 6.72e-01 9.67e+01 angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.22e+00 6.72e-01 9.49e+01 angle pdb=" N PRO B 981 " pdb=" CA PRO B 981 " pdb=" C PRO B 981 " ideal model delta sigma weight residual 110.70 122.56 -11.86 1.22e+00 6.72e-01 9.45e+01 angle pdb=" N PRO A 575 " pdb=" CA PRO A 575 " pdb=" C PRO A 575 " ideal model delta sigma weight residual 111.19 96.87 14.32 1.57e+00 4.06e-01 8.32e+01 ... (remaining 41166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 18249 21.66 - 43.33: 393 43.33 - 64.99: 127 64.99 - 86.65: 37 86.65 - 108.32: 9 Dihedral angle restraints: 18815 sinusoidal: 7794 harmonic: 11021 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 93.00 150.85 -57.85 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CA UNK L 13 " pdb=" C UNK L 13 " pdb=" N UNK L 14 " pdb=" CA UNK L 14 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.51e+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 -132.57 46.57 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 18812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3692 0.113 - 0.226: 1032 0.226 - 0.339: 115 0.339 - 0.451: 16 0.451 - 0.564: 5 Chirality restraints: 4860 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.18e+01 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 -2.57 0.17 2.00e-02 2.50e+03 7.05e+01 ... (remaining 4857 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1403 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG A1403 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1403 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A1403 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG A1403 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1406 " 0.214 2.00e-02 2.50e+03 1.82e-01 4.15e+02 pdb=" C7 NAG A1406 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG A1406 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A1406 " -0.307 2.00e-02 2.50e+03 pdb=" O7 NAG A1406 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C7 NAG R 1 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 8263 2.79 - 3.32: 26591 3.32 - 3.85: 49388 3.85 - 4.37: 60170 4.37 - 4.90: 99855 Nonbonded interactions: 244267 Sorted by model distance: nonbonded pdb=" OG SER B 374 " pdb=" O6 NAG R 1 " model vdw 2.267 3.040 nonbonded pdb=" N ASN J1046 " pdb=" O ASN J1046 " model vdw 2.282 2.496 nonbonded pdb=" N ASN B 371 " pdb=" OD1 ASN B 371 " model vdw 2.284 3.120 nonbonded pdb=" N ASN J 371 " pdb=" OD1 ASN J 371 " model vdw 2.309 3.120 nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.314 3.120 ... (remaining 244262 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 33 or resid 38 through 150 or resid 159 through \ 474 or resid 480 through 504 or resid 517 through 761 or resid 771 through 903 \ or resid 910 through 1405)) selection = (chain 'B' and (resid 15 through 474 or resid 480 through 504 or resid 517 throu \ gh 761 or resid 771 through 903 or resid 910 through 1405)) selection = (chain 'J' and (resid 15 through 150 or resid 159 through 1405)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 18 through 122) selection = chain 'L' } 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: 2.710 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.850 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 0.332 30356 Z= 1.232 Angle : 1.710 14.317 41483 Z= 1.135 Chirality : 0.101 0.564 4860 Planarity : 0.010 0.256 5246 Dihedral : 10.866 108.316 11560 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.26 % Allowed : 0.32 % Favored : 99.42 % 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: 0.54 (0.13), residues: 3505 helix: -0.26 (0.16), residues: 813 sheet: 0.89 (0.17), residues: 847 loop : 0.57 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 998 TYR 0.057 0.008 TYR J1154 PHE 0.032 0.005 PHE J 464 TRP 0.040 0.007 TRP J 655 HIS 0.009 0.002 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.02331 (30231) covalent geometry : angle 1.69457 (41171) SS BOND : bond 0.04991 ( 63) SS BOND : angle 2.85666 ( 126) hydrogen bonds : bond 0.15861 ( 1227) hydrogen bonds : angle 7.27100 ( 3384) link_BETA1-4 : bond 0.02883 ( 21) link_BETA1-4 : angle 3.60071 ( 63) link_NAG-ASN : bond 0.03283 ( 41) link_NAG-ASN : angle 3.07833 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 305 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 33 ILE cc_start: 0.8508 (tt) cc_final: 0.8212 (pp) REVERT: J 82 MET cc_start: 0.9135 (mmm) cc_final: 0.8749 (mmt) REVERT: J 259 THR cc_start: 0.9105 (m) cc_final: 0.8826 (p) REVERT: A 1006 MET cc_start: 0.8969 (mmm) cc_final: 0.8664 (mmm) REVERT: B 1107 ASP cc_start: 0.8405 (m-30) cc_final: 0.8204 (m-30) outliers start: 8 outliers final: 6 residues processed: 313 average time/residue: 0.7731 time to fit residues: 278.7226 Evaluate side-chains 132 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 HIS J 418 GLN J 839 GLN J 849 ASN J1103 GLN J1141 HIS A 219 HIS A 252 HIS A 527 ASN A 849 ASN A1103 GLN A1138 ASN B 160 GLN B 219 HIS B 252 HIS B 849 ASN B1103 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.064087 restraints weight = 57137.259| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.56 r_work: 0.2623 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30356 Z= 0.140 Angle : 0.625 6.856 41483 Z= 0.335 Chirality : 0.046 0.267 4860 Planarity : 0.004 0.049 5246 Dihedral : 7.272 74.385 5400 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.30 % Allowed : 4.90 % Favored : 93.80 % 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: 1.00 (0.14), residues: 3505 helix: 1.49 (0.19), residues: 801 sheet: 0.82 (0.17), residues: 796 loop : 0.35 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 944 TYR 0.025 0.002 TYR A 79 PHE 0.017 0.001 PHE B 67 TRP 0.021 0.002 TRP A 460 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00295 (30231) covalent geometry : angle 0.61291 (41171) SS BOND : bond 0.00293 ( 63) SS BOND : angle 0.90758 ( 126) hydrogen bonds : bond 0.05631 ( 1227) hydrogen bonds : angle 5.62022 ( 3384) link_BETA1-4 : bond 0.00483 ( 21) link_BETA1-4 : angle 1.67331 ( 63) link_NAG-ASN : bond 0.00274 ( 41) link_NAG-ASN : angle 1.96236 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 33 ILE cc_start: 0.8565 (tt) cc_final: 0.8331 (pp) REVERT: J 259 THR cc_start: 0.8888 (m) cc_final: 0.8472 (p) REVERT: J 301 ASP cc_start: 0.8302 (t70) cc_final: 0.7935 (p0) REVERT: J 493 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8943 (ptpp) REVERT: J 1035 ASN cc_start: 0.8302 (t0) cc_final: 0.8022 (t0) REVERT: J 1072 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8742 (mp0) REVERT: J 1194 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8932 (t0) REVERT: A 1006 MET cc_start: 0.9177 (mmm) cc_final: 0.8946 (mmm) REVERT: B 58 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7893 (t70) REVERT: B 194 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7952 (tmm) REVERT: B 346 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 1072 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8577 (mm-30) outliers start: 40 outliers final: 17 residues processed: 218 average time/residue: 0.6405 time to fit residues: 165.1609 Evaluate side-chains 156 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 239 LYS Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 552 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1050 GLU Chi-restraints excluded: chain J residue 1194 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 886 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 261 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 chunk 351 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 ASN J 849 ASN J1053 ASN J1103 GLN A1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.060743 restraints weight = 58299.357| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.53 r_work: 0.2544 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30356 Z= 0.224 Angle : 0.622 8.992 41483 Z= 0.333 Chirality : 0.046 0.283 4860 Planarity : 0.004 0.049 5246 Dihedral : 6.409 68.238 5398 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.78 % Allowed : 6.00 % Favored : 92.21 % 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: 0.71 (0.14), residues: 3505 helix: 1.67 (0.19), residues: 803 sheet: 0.49 (0.17), residues: 783 loop : 0.03 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 413 TYR 0.027 0.002 TYR B 79 PHE 0.015 0.002 PHE B 220 TRP 0.016 0.002 TRP A 460 HIS 0.005 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00529 (30231) covalent geometry : angle 0.60584 (41171) SS BOND : bond 0.00354 ( 63) SS BOND : angle 1.55264 ( 126) hydrogen bonds : bond 0.05622 ( 1227) hydrogen bonds : angle 5.33283 ( 3384) link_BETA1-4 : bond 0.00379 ( 21) link_BETA1-4 : angle 1.50450 ( 63) link_NAG-ASN : bond 0.00339 ( 41) link_NAG-ASN : angle 1.95540 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 19 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8375 (tm) REVERT: J 259 THR cc_start: 0.8931 (m) cc_final: 0.8480 (p) REVERT: J 263 ARG cc_start: 0.7678 (tpm-80) cc_final: 0.7463 (tpm-80) REVERT: J 301 ASP cc_start: 0.8369 (t70) cc_final: 0.8162 (p0) REVERT: J 493 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8965 (ptpp) REVERT: J 944 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7367 (mtp180) REVERT: J 1194 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.9011 (t0) REVERT: J 1217 MET cc_start: 0.9271 (mtm) cc_final: 0.9026 (mpt) REVERT: B 58 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7842 (t70) REVERT: B 346 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8623 (pm20) REVERT: B 1072 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 1107 ASP cc_start: 0.8931 (m-30) cc_final: 0.8630 (m-30) outliers start: 55 outliers final: 21 residues processed: 187 average time/residue: 0.7263 time to fit residues: 157.8376 Evaluate side-chains 158 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 517 ASN Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 892 ASP Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain J residue 1050 GLU Chi-restraints excluded: chain J residue 1194 ASN Chi-restraints excluded: chain J residue 1231 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 257 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN A 849 ASN A1071 GLN A1138 ASN B 483 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.061395 restraints weight = 57420.023| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.54 r_work: 0.2566 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30356 Z= 0.150 Angle : 0.550 7.175 41483 Z= 0.294 Chirality : 0.044 0.289 4860 Planarity : 0.004 0.049 5246 Dihedral : 5.992 74.832 5398 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.49 % Allowed : 6.72 % Favored : 91.79 % 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: 0.70 (0.14), residues: 3505 helix: 1.78 (0.19), residues: 810 sheet: 0.49 (0.17), residues: 785 loop : -0.06 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 263 TYR 0.022 0.001 TYR B 79 PHE 0.012 0.001 PHE J 126 TRP 0.015 0.001 TRP A 460 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00344 (30231) covalent geometry : angle 0.53798 (41171) SS BOND : bond 0.00272 ( 63) SS BOND : angle 1.04897 ( 126) hydrogen bonds : bond 0.04923 ( 1227) hydrogen bonds : angle 5.15313 ( 3384) link_BETA1-4 : bond 0.00390 ( 21) link_BETA1-4 : angle 1.35056 ( 63) link_NAG-ASN : bond 0.00247 ( 41) link_NAG-ASN : angle 1.76826 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 19 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8406 (tm) REVERT: J 22 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8322 (Cg_exo) REVERT: J 259 THR cc_start: 0.8924 (m) cc_final: 0.8482 (p) REVERT: J 493 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8939 (ptpp) REVERT: J 944 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7390 (mtp180) REVERT: J 1194 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.9037 (t0) REVERT: J 1217 MET cc_start: 0.9263 (mtm) cc_final: 0.8593 (mpp) REVERT: A 79 TYR cc_start: 0.8905 (m-80) cc_final: 0.8673 (m-80) REVERT: A 266 ILE cc_start: 0.9011 (tp) cc_final: 0.8795 (pp) REVERT: B 58 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7867 (t70) REVERT: B 346 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8620 (pm20) REVERT: B 883 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8883 (mttm) REVERT: B 1072 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 1107 ASP cc_start: 0.8895 (m-30) cc_final: 0.8568 (m-30) outliers start: 46 outliers final: 20 residues processed: 177 average time/residue: 0.7297 time to fit residues: 151.0080 Evaluate side-chains 156 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain J residue 1050 GLU Chi-restraints excluded: chain J residue 1194 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 889 ASN Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 219 optimal weight: 3.9990 chunk 320 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 162 optimal weight: 0.2980 chunk 363 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN A 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.060032 restraints weight = 57816.459| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.54 r_work: 0.2535 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30356 Z= 0.200 Angle : 0.576 8.048 41483 Z= 0.307 Chirality : 0.045 0.295 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.992 80.662 5398 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.95 % Allowed : 6.62 % Favored : 91.43 % 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: 0.59 (0.14), residues: 3505 helix: 1.82 (0.20), residues: 800 sheet: 0.49 (0.17), residues: 766 loop : -0.22 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 413 TYR 0.023 0.001 TYR B 79 PHE 0.014 0.002 PHE B 220 TRP 0.014 0.001 TRP A 460 HIS 0.005 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00474 (30231) covalent geometry : angle 0.56455 (41171) SS BOND : bond 0.00279 ( 63) SS BOND : angle 0.99677 ( 126) hydrogen bonds : bond 0.05203 ( 1227) hydrogen bonds : angle 5.14376 ( 3384) link_BETA1-4 : bond 0.00386 ( 21) link_BETA1-4 : angle 1.35116 ( 63) link_NAG-ASN : bond 0.00308 ( 41) link_NAG-ASN : angle 1.82774 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 248 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: J 256 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8666 (mpp) REVERT: J 259 THR cc_start: 0.8976 (m) cc_final: 0.8524 (p) REVERT: J 264 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8662 (ttm110) REVERT: J 352 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8433 (tptt) REVERT: J 493 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8917 (ptpp) REVERT: J 944 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: J 1217 MET cc_start: 0.9288 (mtm) cc_final: 0.8545 (mpp) REVERT: A 79 TYR cc_start: 0.8990 (m-80) cc_final: 0.8749 (m-80) REVERT: B 58 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (t70) REVERT: B 346 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: B 883 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8865 (mttm) REVERT: B 889 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8908 (t0) REVERT: B 1072 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8431 (mm-30) REVERT: B 1107 ASP cc_start: 0.8905 (m-30) cc_final: 0.8582 (m-30) outliers start: 60 outliers final: 28 residues processed: 182 average time/residue: 0.7330 time to fit residues: 155.3613 Evaluate side-chains 165 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain J residue 1050 GLU Chi-restraints excluded: chain J residue 1231 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 889 ASN Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 122 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 334 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 340 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 606 HIS J 663 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.062148 restraints weight = 57407.431| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.51 r_work: 0.2583 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30356 Z= 0.109 Angle : 0.507 7.534 41483 Z= 0.272 Chirality : 0.043 0.262 4860 Planarity : 0.004 0.052 5246 Dihedral : 5.606 83.119 5398 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.59 % Allowed : 7.17 % Favored : 91.24 % 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: 0.67 (0.14), residues: 3505 helix: 1.90 (0.20), residues: 813 sheet: 0.54 (0.17), residues: 775 loop : -0.18 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.019 0.001 TYR B 79 PHE 0.012 0.001 PHE J 980 TRP 0.013 0.001 TRP J 460 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00236 (30231) covalent geometry : angle 0.49759 (41171) SS BOND : bond 0.00189 ( 63) SS BOND : angle 0.69438 ( 126) hydrogen bonds : bond 0.04366 ( 1227) hydrogen bonds : angle 4.93631 ( 3384) link_BETA1-4 : bond 0.00400 ( 21) link_BETA1-4 : angle 1.26569 ( 63) link_NAG-ASN : bond 0.00234 ( 41) link_NAG-ASN : angle 1.60976 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 248 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7676 (mmt) REVERT: J 259 THR cc_start: 0.8886 (m) cc_final: 0.8458 (p) REVERT: J 266 ILE cc_start: 0.8623 (tp) cc_final: 0.8352 (pp) REVERT: J 944 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7497 (mtp180) REVERT: A 79 TYR cc_start: 0.8871 (m-80) cc_final: 0.8652 (m-80) REVERT: A 569 ASP cc_start: 0.8799 (m-30) cc_final: 0.8565 (m-30) REVERT: B 58 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7872 (t70) REVERT: B 346 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: B 547 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8344 (tptp) REVERT: B 883 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8775 (mtmm) REVERT: B 1072 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 1107 ASP cc_start: 0.8798 (m-30) cc_final: 0.8442 (m-30) outliers start: 49 outliers final: 18 residues processed: 180 average time/residue: 0.6965 time to fit residues: 146.8628 Evaluate side-chains 151 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 239 LYS Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.4980 chunk 182 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 366 optimal weight: 40.0000 chunk 252 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN ** A1103 GLN ** 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 = 0.3102 r_free = 0.3102 target = 0.081903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.061740 restraints weight = 57682.837| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.52 r_work: 0.2576 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30356 Z= 0.128 Angle : 0.513 7.682 41483 Z= 0.274 Chirality : 0.043 0.258 4860 Planarity : 0.004 0.052 5246 Dihedral : 5.528 84.599 5398 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 7.53 % Favored : 90.85 % 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: 0.66 (0.14), residues: 3505 helix: 1.97 (0.20), residues: 808 sheet: 0.53 (0.17), residues: 776 loop : -0.22 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 264 TYR 0.019 0.001 TYR A 79 PHE 0.011 0.001 PHE J 126 TRP 0.012 0.001 TRP A 460 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00292 (30231) covalent geometry : angle 0.50303 (41171) SS BOND : bond 0.00204 ( 63) SS BOND : angle 0.75519 ( 126) hydrogen bonds : bond 0.04440 ( 1227) hydrogen bonds : angle 4.88448 ( 3384) link_BETA1-4 : bond 0.00383 ( 21) link_BETA1-4 : angle 1.21821 ( 63) link_NAG-ASN : bond 0.00274 ( 41) link_NAG-ASN : angle 1.64326 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 248 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: J 256 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8875 (mpp) REVERT: J 259 THR cc_start: 0.8892 (m) cc_final: 0.8430 (p) REVERT: J 493 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (ptpp) REVERT: J 944 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7477 (mtp180) REVERT: J 1103 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: A 901 CYS cc_start: 0.7649 (m) cc_final: 0.7385 (m) REVERT: B 58 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7887 (t70) REVERT: B 346 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: B 380 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8783 (tm-30) REVERT: B 547 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8306 (tptp) REVERT: B 883 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8895 (mttm) REVERT: B 1072 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 1107 ASP cc_start: 0.8799 (m-30) cc_final: 0.8446 (m-30) outliers start: 50 outliers final: 25 residues processed: 170 average time/residue: 0.6910 time to fit residues: 137.6153 Evaluate side-chains 166 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain J residue 1103 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 311 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 369 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN ** J 849 ASN ** 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 = 0.3094 r_free = 0.3094 target = 0.081680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.061644 restraints weight = 58106.408| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.49 r_work: 0.2560 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30356 Z= 0.153 Angle : 0.527 7.831 41483 Z= 0.281 Chirality : 0.043 0.271 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.613 88.409 5398 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.59 % Allowed : 7.75 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.14), residues: 3505 helix: 2.03 (0.20), residues: 796 sheet: 0.53 (0.17), residues: 776 loop : -0.24 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 264 TYR 0.026 0.001 TYR A 79 PHE 0.012 0.001 PHE B 220 TRP 0.012 0.001 TRP A 460 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00356 (30231) covalent geometry : angle 0.51644 (41171) SS BOND : bond 0.00238 ( 63) SS BOND : angle 0.79245 ( 126) hydrogen bonds : bond 0.04654 ( 1227) hydrogen bonds : angle 4.92686 ( 3384) link_BETA1-4 : bond 0.00426 ( 21) link_BETA1-4 : angle 1.26709 ( 63) link_NAG-ASN : bond 0.00295 ( 41) link_NAG-ASN : angle 1.67890 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 248 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7712 (mmt) REVERT: J 259 THR cc_start: 0.8917 (m) cc_final: 0.8478 (p) REVERT: J 266 ILE cc_start: 0.8660 (tp) cc_final: 0.8443 (pp) REVERT: J 352 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8516 (tptt) REVERT: J 419 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7904 (mm) REVERT: J 493 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9094 (ptpp) REVERT: J 944 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7477 (mtp180) REVERT: J 1103 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: A 901 CYS cc_start: 0.7657 (m) cc_final: 0.7386 (m) REVERT: B 58 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7878 (t70) REVERT: B 346 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: B 547 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8271 (tptp) REVERT: B 883 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8891 (mttm) REVERT: B 1072 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 1107 ASP cc_start: 0.8819 (m-30) cc_final: 0.8471 (m-30) outliers start: 49 outliers final: 29 residues processed: 172 average time/residue: 0.7203 time to fit residues: 143.8657 Evaluate side-chains 171 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain J residue 1103 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 347 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 353 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN ** J 849 ASN ** 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 = 0.3079 r_free = 0.3079 target = 0.080767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.060414 restraints weight = 57541.930| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.53 r_work: 0.2542 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30356 Z= 0.180 Angle : 0.550 8.275 41483 Z= 0.292 Chirality : 0.044 0.280 4860 Planarity : 0.004 0.055 5246 Dihedral : 5.753 89.603 5398 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.56 % Allowed : 7.85 % Favored : 90.59 % 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: 0.57 (0.14), residues: 3505 helix: 1.98 (0.20), residues: 790 sheet: 0.52 (0.17), residues: 777 loop : -0.32 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 264 TYR 0.032 0.001 TYR A 79 PHE 0.013 0.001 PHE B 220 TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00426 (30231) covalent geometry : angle 0.53900 (41171) SS BOND : bond 0.00265 ( 63) SS BOND : angle 0.85475 ( 126) hydrogen bonds : bond 0.04929 ( 1227) hydrogen bonds : angle 5.01519 ( 3384) link_BETA1-4 : bond 0.00349 ( 21) link_BETA1-4 : angle 1.25501 ( 63) link_NAG-ASN : bond 0.00307 ( 41) link_NAG-ASN : angle 1.74298 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 248 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7728 (mmt) REVERT: J 259 THR cc_start: 0.8956 (m) cc_final: 0.8527 (p) REVERT: J 352 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8670 (tptt) REVERT: J 419 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7814 (mm) REVERT: J 493 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9082 (ptpp) REVERT: J 944 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7472 (mtp180) REVERT: A 569 ASP cc_start: 0.8853 (m-30) cc_final: 0.8629 (m-30) REVERT: A 901 CYS cc_start: 0.7660 (m) cc_final: 0.7395 (m) REVERT: B 58 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7907 (t70) REVERT: B 346 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: B 547 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8259 (tptp) REVERT: B 883 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8771 (mtmm) REVERT: B 1072 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 1107 ASP cc_start: 0.8847 (m-30) cc_final: 0.8506 (m-30) outliers start: 48 outliers final: 30 residues processed: 175 average time/residue: 0.7208 time to fit residues: 146.9874 Evaluate side-chains 167 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 349 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 62 optimal weight: 0.0470 chunk 231 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN ** J 849 ASN ** 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 = 0.3074 r_free = 0.3074 target = 0.080306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.060195 restraints weight = 58365.432| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.47 r_work: 0.2537 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30356 Z= 0.184 Angle : 0.555 8.292 41483 Z= 0.295 Chirality : 0.044 0.285 4860 Planarity : 0.004 0.055 5246 Dihedral : 5.776 88.053 5398 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.33 % Allowed : 8.14 % Favored : 90.53 % 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: 0.52 (0.14), residues: 3505 helix: 1.95 (0.20), residues: 793 sheet: 0.53 (0.17), residues: 767 loop : -0.39 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 264 TYR 0.032 0.001 TYR A 79 PHE 0.013 0.001 PHE B 220 TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00436 (30231) covalent geometry : angle 0.54437 (41171) SS BOND : bond 0.00263 ( 63) SS BOND : angle 0.84908 ( 126) hydrogen bonds : bond 0.04948 ( 1227) hydrogen bonds : angle 5.03282 ( 3384) link_BETA1-4 : bond 0.00367 ( 21) link_BETA1-4 : angle 1.24810 ( 63) link_NAG-ASN : bond 0.00292 ( 41) link_NAG-ASN : angle 1.73705 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 259 THR cc_start: 0.8987 (m) cc_final: 0.8581 (p) REVERT: J 419 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7830 (mm) REVERT: J 493 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9130 (ptpp) REVERT: J 944 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: A 901 CYS cc_start: 0.7677 (m) cc_final: 0.7420 (m) REVERT: B 58 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (t70) REVERT: B 547 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8295 (tptp) REVERT: B 883 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8775 (mtmm) REVERT: B 1072 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8459 (mm-30) REVERT: B 1107 ASP cc_start: 0.8889 (m-30) cc_final: 0.8580 (m-30) outliers start: 41 outliers final: 29 residues processed: 163 average time/residue: 0.7340 time to fit residues: 139.6256 Evaluate side-chains 160 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 493 LYS Chi-restraints excluded: chain J residue 724 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 944 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1226 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 169 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.0070 chunk 53 optimal weight: 10.0000 chunk 349 optimal weight: 0.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 663 ASN ** J 849 ASN ** 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 = 0.3079 r_free = 0.3079 target = 0.080657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.060531 restraints weight = 58479.051| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.48 r_work: 0.2550 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30356 Z= 0.159 Angle : 0.542 8.149 41483 Z= 0.289 Chirality : 0.044 0.278 4860 Planarity : 0.004 0.055 5246 Dihedral : 5.684 86.645 5398 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.36 % Allowed : 8.14 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3505 helix: 1.92 (0.19), residues: 806 sheet: 0.54 (0.17), residues: 767 loop : -0.38 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 264 TYR 0.033 0.001 TYR A 546 PHE 0.012 0.001 PHE B 220 TRP 0.013 0.001 TRP A 460 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00373 (30231) covalent geometry : angle 0.53250 (41171) SS BOND : bond 0.00242 ( 63) SS BOND : angle 0.78825 ( 126) hydrogen bonds : bond 0.04755 ( 1227) hydrogen bonds : angle 4.98462 ( 3384) link_BETA1-4 : bond 0.00369 ( 21) link_BETA1-4 : angle 1.21561 ( 63) link_NAG-ASN : bond 0.00278 ( 41) link_NAG-ASN : angle 1.68713 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7832.20 seconds wall clock time: 134 minutes 24.30 seconds (8064.30 seconds total)