Starting phenix.real_space_refine on Fri Mar 6 09:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.map" model { file = "/net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb3_24968/03_2026/7sb3_24968.cif" } resolution = 3.3 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 18691 2.51 5 N 4797 2.21 5 O 5774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 211 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: 29451 Number of models: 1 Model: "" Number of chains: 22 Chain: "J" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9198 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 51, 'TRANS': 1131} Chain breaks: 5 Chain: "A" Number of atoms: 9168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9168 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 51, 'TRANS': 1126} Chain breaks: 6 Chain: "B" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9185 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 53, 'TRANS': 1128} Chain breaks: 5 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 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: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "J" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {'8Z9': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'8Z9': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.86, per 1000 atoms: 0.23 Number of scatterers: 29451 At special positions: 0 Unit cell: (151.41, 177.16, 166.86, 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 5774 8.00 N 4797 7.00 C 18691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.02 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.04 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.09 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=2.03 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.03 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.04 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=2.04 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=2.13 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.02 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.02 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=2.10 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.03 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.03 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.09 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.09 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.04 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.10 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=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.16 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.08 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.04 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.06 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.10 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.04 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.10 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.04 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.06 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 449 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A1193 " " NAG A1407 " - " ASN A 675 " " NAG A1408 " - " ASN A 648 " " NAG A1409 " - " ASN A1223 " " NAG B1401 " - " ASN B 137 " " NAG B1402 " - " ASN B 212 " " NAG B1403 " - " ASN B 449 " " NAG B1404 " - " ASN B 713 " " NAG B1405 " - " ASN B 787 " " NAG B1406 " - " ASN B 695 " " NAG B1407 " - " ASN B 648 " " NAG B1408 " - " ASN B 936 " " NAG B1409 " - " ASN B1223 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 738 " " NAG F 1 " - " ASN J 206 " " NAG G 1 " - " ASN A 137 " " NAG I 1 " - " ASN A 371 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 449 " " NAG J1403 " - " ASN J 713 " " NAG J1404 " - " ASN J 787 " " NAG J1405 " - " ASN J 936 " " NAG J1406 " - " ASN J1193 " " NAG J1407 " - " ASN J 675 " " NAG J1408 " - " ASN J 695 " " NAG J1409 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A 206 " " NAG N 1 " - " ASN A 695 " " NAG O 1 " - " ASN B 371 " " NAG P 1 " - " ASN B 738 " " NAG Q 1 " - " ASN B1193 " " NAG R 1 " - " ASN B 206 " " NAG S 1 " - " ASN B 675 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.3 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: 7044 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 75 sheets defined 26.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 181 through 185 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'J' and resid 301 through 310 Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 360 removed outlier: 3.563A pdb=" N TRP J 360 " --> pdb=" O PRO J 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 357 through 360' Processing helix chain 'J' and resid 371 through 379 removed outlier: 4.125A pdb=" N SER J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 394 Processing helix chain 'J' and resid 413 through 418 Processing helix chain 'J' and resid 423 through 429 Processing helix chain 'J' and resid 448 through 450 No H-bonds generated for 'chain 'J' and resid 448 through 450' Processing helix chain 'J' and resid 461 through 465 Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'J' and resid 538 through 542 removed outlier: 4.335A pdb=" N PHE J 542 " --> pdb=" O PRO J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 714 Processing helix chain 'J' and resid 825 through 830 Processing helix chain 'J' and resid 833 through 841 Processing helix chain 'J' and resid 842 through 846 removed outlier: 6.408A pdb=" N SER J 845 " --> pdb=" O GLU J 842 " (cutoff:3.500A) Processing helix chain 'J' and resid 847 through 874 Processing helix chain 'J' and resid 881 through 884 Processing helix chain 'J' and resid 913 through 922 removed outlier: 3.978A pdb=" N LYS J 922 " --> pdb=" O LEU J 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 934 Processing helix chain 'J' and resid 945 through 952 Processing helix chain 'J' and resid 963 through 976 Processing helix chain 'J' and resid 977 through 979 No H-bonds generated for 'chain 'J' and resid 977 through 979' Processing helix chain 'J' and resid 984 through 989 removed outlier: 3.779A pdb=" N GLY J 988 " --> pdb=" O ALA J 985 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 989 " --> pdb=" O ALA J 986 " (cutoff:3.500A) Processing helix chain 'J' and resid 990 through 1001 Processing helix chain 'J' and resid 1005 through 1011 removed outlier: 3.546A pdb=" N GLN J1011 " --> pdb=" O ASP J1007 " (cutoff:3.500A) Processing helix chain 'J' and resid 1012 through 1029 Processing helix chain 'J' and resid 1035 through 1059 removed outlier: 3.852A pdb=" N LEU J1059 " --> pdb=" O LEU J1055 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1077 removed outlier: 3.568A pdb=" N SER J1075 " --> pdb=" O GLN J1071 " (cutoff:3.500A) Processing helix chain 'J' and resid 1078 through 1125 removed outlier: 4.910A 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 263 through 267 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.529A pdb=" N TRP A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 371 through 379 removed outlier: 5.024A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.567A 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 423 through 428 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.579A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 removed outlier: 3.880A pdb=" N GLN A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 873 removed outlier: 4.000A 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 922 removed outlier: 4.139A pdb=" N LYS A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 935 removed outlier: 3.521A pdb=" N ASN A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 980 removed outlier: 4.110A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1012 removed outlier: 3.526A pdb=" N LEU A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1036 through 1057 removed outlier: 4.185A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 4.967A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 removed outlier: 3.876A 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 345 through 350 Processing helix chain 'B' and resid 357 through 360 removed outlier: 3.666A pdb=" N TRP B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 371 through 379 removed outlier: 5.085A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (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 459 through 464 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.997A pdb=" N PHE B 542 " --> pdb=" O PRO B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 843 through 874 removed outlier: 3.604A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.044A 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 945 through 953 Processing helix chain 'B' and resid 963 through 980 removed outlier: 3.541A pdb=" N THR B 975 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1001 removed outlier: 3.739A pdb=" N GLN B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1011 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1035 through 1060 removed outlier: 3.522A pdb=" N VAL B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1125 removed outlier: 5.052A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'L' and resid 59 through 63 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'J' and resid 58 through 60 removed outlier: 7.031A pdb=" N ASP J 58 " --> pdb=" O GLN A 656 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN A 657 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE A 669 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 65 through 73 removed outlier: 4.336A pdb=" N GLY J 106 " --> pdb=" O LEU J 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 242 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'J' and resid 85 through 86 removed outlier: 6.552A pdb=" N THR J 178 " --> pdb=" O THR J 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 101 through 102 removed outlier: 3.690A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 114 through 118 Processing sheet with id=AA7, first strand: chain 'J' and resid 318 through 321 Processing sheet with id=AA8, first strand: chain 'J' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'J' and resid 332 through 335 removed outlier: 5.605A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU J 658 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 353 through 355 Processing sheet with id=AB2, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.963A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER J 438 " --> pdb=" O CYS J 386 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS J 386 " --> pdb=" O SER J 438 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN J 440 " --> pdb=" O PHE J 384 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE J 384 " --> pdb=" O GLN J 440 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR J 442 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.963A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 398 through 399 Processing sheet with id=AB5, first strand: chain 'J' and resid 484 through 488 Processing sheet with id=AB6, first strand: chain 'J' and resid 491 through 493 removed outlier: 4.410A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 520 through 521 Processing sheet with id=AB8, first strand: chain 'J' and resid 565 through 566 Processing sheet with id=AB9, first strand: chain 'J' and resid 737 through 743 removed outlier: 6.578A pdb=" N TYR J 737 " --> pdb=" O PHE J 775 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ASN J 777 " --> pdb=" O TYR J 737 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER J 739 " --> pdb=" O ASN J 777 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR J 755 " --> pdb=" O VAL J 751 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 784 through 786 removed outlier: 5.983A pdb=" N ASN J 784 " --> pdb=" O LEU B 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 797 through 815 removed outlier: 6.844A pdb=" N GLU J 798 " --> pdb=" O LYS J1169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS J1169 " --> pdb=" O GLU J 798 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN J 800 " --> pdb=" O THR J1167 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR J1167 " --> pdb=" O GLN J 800 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR J1165 " --> pdb=" O PRO J 802 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU J 804 " --> pdb=" O THR J1163 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY J1152 " --> pdb=" O ASN J1148 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN J1148 " --> pdb=" O GLY J1152 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR J1154 " --> pdb=" O VAL J1146 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL J1146 " --> pdb=" O TYR J1154 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE J1156 " --> pdb=" O SER J1144 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER J1144 " --> pdb=" O ILE J1156 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE J1158 " --> pdb=" O ILE J1142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.117A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 877 through 879 Processing sheet with id=AC5, first strand: chain 'J' and resid 889 through 890 Processing sheet with id=AC6, first strand: chain 'J' and resid 1214 through 1217 Processing sheet with id=AC7, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id=AC8, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AC9, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.571A pdb=" N ALA A 43 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 106 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 64 through 73 Processing sheet with id=AD2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.752A pdb=" N GLY B 668 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.850A pdb=" N GLY A 86 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 101 through 102 removed outlier: 4.010A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AD6, first strand: chain 'A' and resid 318 through 326 removed outlier: 5.256A pdb=" N VAL A 688 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY A 324 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A 686 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG A 687 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG A 704 " --> pdb=" O ARG A 687 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.713A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.992A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.992A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AE2, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AE3, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AE4, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AE5, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AE6, first strand: chain 'A' and resid 737 through 744 removed outlier: 6.565A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 749 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 797 through 815 removed outlier: 6.925A pdb=" N GLU A 798 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS A1169 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN A 800 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A1167 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A1165 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU A 804 " --> pdb=" O THR A1163 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN A1148 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A1154 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A1146 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A1156 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A1144 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A1158 " --> pdb=" O ILE A1142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.292A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AF1, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AF2, first strand: chain 'A' and resid 1214 through 1217 Processing sheet with id=AF3, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id=AF4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.124A pdb=" N SER B 29 " --> pdb=" O LEU B 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 39 through 44 removed outlier: 3.920A pdb=" N SER B 39 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 79 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.856A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AF8, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AF9, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.484A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.574A pdb=" N CYS B 732 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AG3, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.647A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.561A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER B 438 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N CYS B 386 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN B 440 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 384 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 442 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.561A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AG7, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AG8, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AG9, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AH1, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AH2, first strand: chain 'B' and resid 737 through 744 removed outlier: 7.013A pdb=" N TYR B 737 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN B 777 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N SER B 739 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 797 through 802 Processing sheet with id=AH4, first strand: chain 'B' and resid 805 through 815 removed outlier: 4.104A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B1160 " --> pdb=" O HIS B1141 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS B1141 " --> pdb=" O TYR B1160 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.286A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AH7, first strand: chain 'B' and resid 1214 through 1217 Processing sheet with id=AH8, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id=AH9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.573A pdb=" N UNK H 10 " --> pdb=" O UNK H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AI3, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.573A pdb=" N UNK L 10 " --> pdb=" O UNK L 105 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3147 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: 8.20 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7714 1.33 - 1.47: 9841 1.47 - 1.61: 12282 1.61 - 1.75: 16 1.75 - 1.89: 230 Bond restraints: 30083 Sorted by residual: bond pdb=" CB PHE A 669 " pdb=" CG PHE A 669 " ideal model delta sigma weight residual 1.502 1.350 0.152 2.30e-02 1.89e+03 4.38e+01 bond pdb=" CB HIS A 193 " pdb=" CG HIS A 193 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CB HIS J 219 " pdb=" CG HIS J 219 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS A 483 " pdb=" CG HIS A 483 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.38e+01 ... (remaining 30078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 36494 2.67 - 5.34: 3909 5.34 - 8.01: 486 8.01 - 10.68: 72 10.68 - 13.35: 8 Bond angle restraints: 40969 Sorted by residual: angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.80 -12.10 1.22e+00 6.72e-01 9.84e+01 angle pdb=" N PHE J 240 " pdb=" CA PHE J 240 " pdb=" C PHE J 240 " ideal model delta sigma weight residual 111.33 123.13 -11.80 1.21e+00 6.83e-01 9.51e+01 angle pdb=" C LYS J 473 " pdb=" N PRO J 474 " pdb=" CA PRO J 474 " ideal model delta sigma weight residual 119.76 128.89 -9.13 1.03e+00 9.43e-01 7.86e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 128.54 -8.51 9.90e-01 1.02e+00 7.39e+01 angle pdb=" C ALA J 314 " pdb=" N PRO J 315 " pdb=" CA PRO J 315 " ideal model delta sigma weight residual 119.66 125.88 -6.22 7.30e-01 1.88e+00 7.26e+01 ... (remaining 40964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 18085 21.75 - 43.49: 402 43.49 - 65.23: 137 65.23 - 86.98: 23 86.98 - 108.72: 8 Dihedral angle restraints: 18655 sinusoidal: 7669 harmonic: 10986 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual 93.00 44.86 48.14 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA UNK L 30 " pdb=" C UNK L 30 " pdb=" N UNK L 31 " pdb=" CA UNK L 31 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" C TRP A 460 " pdb=" N TRP A 460 " pdb=" CA TRP A 460 " pdb=" CB TRP A 460 " ideal model delta harmonic sigma weight residual -122.60 -135.61 13.01 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 18652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3622 0.104 - 0.207: 1059 0.207 - 0.311: 118 0.311 - 0.415: 15 0.415 - 0.519: 3 Chirality restraints: 4817 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.43e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.21e+01 ... (remaining 4814 not shown) Planarity restraints: 5270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1405 " -0.333 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG B1405 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1405 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B1405 " 0.492 2.00e-02 2.50e+03 pdb=" O7 NAG B1405 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1403 " -0.228 2.00e-02 2.50e+03 1.90e-01 4.52e+02 pdb=" C7 NAG B1403 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1403 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG B1403 " 0.314 2.00e-02 2.50e+03 pdb=" O7 NAG B1403 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 936 " -0.063 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C ASN B 936 " 0.223 2.00e-02 2.50e+03 pdb=" O ASN B 936 " -0.085 2.00e-02 2.50e+03 pdb=" N CYS B 937 " -0.075 2.00e-02 2.50e+03 ... (remaining 5267 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8928 2.82 - 3.34: 26395 3.34 - 3.86: 48409 3.86 - 4.38: 57300 4.38 - 4.90: 94226 Nonbonded interactions: 235258 Sorted by model distance: nonbonded pdb=" N ASN B 935 " pdb=" O ASN B 935 " model vdw 2.294 2.496 nonbonded pdb=" N ASN J 935 " pdb=" O ASN J 935 " model vdw 2.307 2.496 nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.319 3.120 nonbonded pdb=" NZ LYS J 85 " pdb=" OG1 THR J 87 " model vdw 2.343 3.120 nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.345 2.496 ... (remaining 235253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 23 or resid 25 or resid 39 through 761 or resid \ 771 through 901 or resid 910 through 1232 or resid 1401 through 1408)) selection = (chain 'B' and (resid 15 through 23 or resid 29 or resid 39 through 151 or resid \ 159 through 195 or resid 199 through 505 or resid 517 through 901 or resid 910 \ through 1232 or resid 1402 through 1409)) selection = (chain 'J' and (resid 15 through 23 or resid 25 or resid 39 through 151 or resid \ 159 through 195 or resid 199 through 505 or resid 517 through 761 or resid 771 \ through 901 or resid 910 through 1232 or resid 1402 through 1409)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'H' and resid 13 through 114) 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.670 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.019 0.152 30202 Z= 1.002 Angle : 1.750 13.349 41263 Z= 1.159 Chirality : 0.093 0.519 4817 Planarity : 0.010 0.282 5229 Dihedral : 10.581 108.724 11422 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.36 % Allowed : 0.71 % Favored : 98.93 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 3505 helix: -0.68 (0.16), residues: 816 sheet: 0.94 (0.16), residues: 806 loop : 0.28 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J1093 TYR 0.067 0.008 TYR B 667 PHE 0.030 0.005 PHE J 542 TRP 0.040 0.008 TRP A 655 HIS 0.012 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.01871 (30083) covalent geometry : angle 1.74267 (40969) SS BOND : bond 0.03341 ( 63) SS BOND : angle 2.48218 ( 126) hydrogen bonds : bond 0.16991 ( 1130) hydrogen bonds : angle 7.63430 ( 3147) link_BETA1-4 : bond 0.02830 ( 15) link_BETA1-4 : angle 3.49448 ( 45) link_NAG-ASN : bond 0.02882 ( 41) link_NAG-ASN : angle 2.29643 ( 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 386 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 375 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 389 ILE cc_start: 0.8754 (mm) cc_final: 0.8544 (tt) REVERT: A 938 THR cc_start: 0.8584 (p) cc_final: 0.8364 (p) REVERT: B 444 ASN cc_start: 0.7825 (m-40) cc_final: 0.7188 (m-40) REVERT: B 886 VAL cc_start: 0.8308 (t) cc_final: 0.8035 (p) outliers start: 11 outliers final: 7 residues processed: 386 average time/residue: 0.1992 time to fit residues: 122.1401 Evaluate side-chains 146 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 187 HIS J 219 HIS ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 724 ASN J 800 GLN J1091 ASN J1103 GLN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 418 GLN A 444 ASN A 598 ASN A 724 ASN A 809 ASN A 849 ASN A 874 ASN A1061 ASN A1071 GLN A1138 ASN B 252 HIS B 849 ASN B 865 GLN B1103 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056542 restraints weight = 84696.232| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.01 r_work: 0.2737 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30202 Z= 0.173 Angle : 0.689 17.015 41263 Z= 0.358 Chirality : 0.046 0.208 4817 Planarity : 0.004 0.049 5229 Dihedral : 7.237 69.405 5264 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.01 % Allowed : 4.22 % Favored : 94.78 % 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: 0.64 (0.14), residues: 3505 helix: 1.08 (0.19), residues: 789 sheet: 0.70 (0.17), residues: 788 loop : 0.13 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 944 TYR 0.019 0.002 TYR B 443 PHE 0.020 0.002 PHE A 286 TRP 0.020 0.002 TRP B 460 HIS 0.018 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00376 (30083) covalent geometry : angle 0.67292 (40969) SS BOND : bond 0.01040 ( 63) SS BOND : angle 0.95412 ( 126) hydrogen bonds : bond 0.05680 ( 1130) hydrogen bonds : angle 5.61471 ( 3147) link_BETA1-4 : bond 0.00551 ( 15) link_BETA1-4 : angle 1.88947 ( 45) link_NAG-ASN : bond 0.00434 ( 41) link_NAG-ASN : angle 2.47269 ( 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 194 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8030 (tpp) cc_final: 0.7394 (tpp) REVERT: A 1138 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7608 (t0) REVERT: B 859 GLU cc_start: 0.8629 (tp30) cc_final: 0.8308 (tt0) outliers start: 31 outliers final: 16 residues processed: 188 average time/residue: 0.1791 time to fit residues: 56.6671 Evaluate side-chains 128 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 293 PHE Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 308 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 chunk 274 optimal weight: 5.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 252 HIS J 388 ASN J 421 ASN J 429 ASN J 444 ASN J 849 ASN J1000 ASN J1147 GLN A 663 ASN A1103 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.055014 restraints weight = 84505.273| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.03 r_work: 0.2697 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30202 Z= 0.137 Angle : 0.571 16.322 41263 Z= 0.300 Chirality : 0.043 0.245 4817 Planarity : 0.004 0.043 5229 Dihedral : 6.083 59.213 5256 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.23 % Allowed : 4.80 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3505 helix: 1.47 (0.19), residues: 795 sheet: 0.68 (0.17), residues: 789 loop : -0.03 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 944 TYR 0.014 0.001 TYR J 79 PHE 0.026 0.001 PHE B 268 TRP 0.013 0.001 TRP J 192 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00298 (30083) covalent geometry : angle 0.55920 (40969) SS BOND : bond 0.00259 ( 63) SS BOND : angle 0.80573 ( 126) hydrogen bonds : bond 0.04726 ( 1130) hydrogen bonds : angle 5.08960 ( 3147) link_BETA1-4 : bond 0.00517 ( 15) link_BETA1-4 : angle 1.52612 ( 45) link_NAG-ASN : bond 0.00310 ( 41) link_NAG-ASN : angle 1.90278 ( 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 162 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7999 (m-80) cc_final: 0.7600 (m-80) REVERT: A 122 MET cc_start: 0.8002 (tpp) cc_final: 0.7267 (tpp) REVERT: A 191 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8917 (tp) REVERT: B 595 ASP cc_start: 0.8513 (t0) cc_final: 0.8309 (t0) REVERT: B 859 GLU cc_start: 0.8527 (tp30) cc_final: 0.8278 (tt0) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 0.1667 time to fit residues: 45.7098 Evaluate side-chains 131 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 356 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 328 optimal weight: 0.0060 chunk 211 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 359 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1011 GLN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 996 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.053081 restraints weight = 84105.574| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.01 r_work: 0.2643 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30202 Z= 0.148 Angle : 0.560 16.392 41263 Z= 0.291 Chirality : 0.043 0.206 4817 Planarity : 0.004 0.044 5229 Dihedral : 5.586 56.794 5254 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.07 % Allowed : 5.42 % Favored : 93.51 % 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: 0.63 (0.14), residues: 3505 helix: 1.66 (0.20), residues: 787 sheet: 0.65 (0.18), residues: 781 loop : -0.15 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 80 TYR 0.013 0.001 TYR J 667 PHE 0.027 0.001 PHE B 268 TRP 0.010 0.001 TRP B 460 HIS 0.015 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00336 (30083) covalent geometry : angle 0.55064 (40969) SS BOND : bond 0.00279 ( 63) SS BOND : angle 0.72983 ( 126) hydrogen bonds : bond 0.04381 ( 1130) hydrogen bonds : angle 4.86597 ( 3147) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.37782 ( 45) link_NAG-ASN : bond 0.00332 ( 41) link_NAG-ASN : angle 1.77185 ( 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 155 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8034 (m-80) cc_final: 0.7771 (m-80) REVERT: A 122 MET cc_start: 0.8093 (tpp) cc_final: 0.7619 (tpp) REVERT: B 595 ASP cc_start: 0.8554 (t0) cc_final: 0.8314 (t0) REVERT: B 859 GLU cc_start: 0.8560 (tp30) cc_final: 0.8158 (tt0) REVERT: B 1006 MET cc_start: 0.9200 (mmm) cc_final: 0.8923 (tpp) REVERT: B 1078 ASP cc_start: 0.7747 (t0) cc_final: 0.7480 (p0) outliers start: 33 outliers final: 22 residues processed: 151 average time/residue: 0.1623 time to fit residues: 42.7518 Evaluate side-chains 129 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 270 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 358 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 251 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 849 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052195 restraints weight = 84287.018| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.02 r_work: 0.2619 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30202 Z= 0.148 Angle : 0.540 15.620 41263 Z= 0.282 Chirality : 0.042 0.219 4817 Planarity : 0.004 0.045 5229 Dihedral : 5.405 54.276 5254 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.17 % Allowed : 5.97 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3505 helix: 1.73 (0.20), residues: 786 sheet: 0.56 (0.18), residues: 796 loop : -0.24 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.018 0.001 TYR A 79 PHE 0.027 0.001 PHE B 268 TRP 0.018 0.001 TRP J 192 HIS 0.018 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00341 (30083) covalent geometry : angle 0.53131 (40969) SS BOND : bond 0.00220 ( 63) SS BOND : angle 0.69259 ( 126) hydrogen bonds : bond 0.04294 ( 1130) hydrogen bonds : angle 4.79936 ( 3147) link_BETA1-4 : bond 0.00365 ( 15) link_BETA1-4 : angle 1.33830 ( 45) link_NAG-ASN : bond 0.00291 ( 41) link_NAG-ASN : angle 1.65986 ( 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 149 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7546 (mt0) cc_final: 0.7188 (mp10) REVERT: J 191 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 122 MET cc_start: 0.8098 (tpp) cc_final: 0.7667 (tpp) REVERT: A 191 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8803 (tt) REVERT: A 682 SER cc_start: 0.9299 (m) cc_final: 0.9089 (p) REVERT: A 1057 GLN cc_start: 0.8860 (mt0) cc_final: 0.8657 (tm-30) REVERT: B 595 ASP cc_start: 0.8529 (t0) cc_final: 0.8324 (t0) REVERT: B 859 GLU cc_start: 0.8617 (tp30) cc_final: 0.8359 (tt0) outliers start: 36 outliers final: 24 residues processed: 148 average time/residue: 0.1633 time to fit residues: 41.1047 Evaluate side-chains 131 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 239 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 chunk 356 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 372 optimal weight: 30.0000 chunk 195 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 361 optimal weight: 20.0000 chunk 335 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 719 GLN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051300 restraints weight = 83875.480| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.99 r_work: 0.2594 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30202 Z= 0.164 Angle : 0.552 16.203 41263 Z= 0.286 Chirality : 0.043 0.210 4817 Planarity : 0.004 0.046 5229 Dihedral : 5.426 54.612 5254 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.27 % Allowed : 6.00 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3505 helix: 1.75 (0.20), residues: 786 sheet: 0.47 (0.18), residues: 779 loop : -0.34 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 944 TYR 0.013 0.001 TYR B 443 PHE 0.027 0.001 PHE B 268 TRP 0.010 0.001 TRP B 460 HIS 0.012 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00379 (30083) covalent geometry : angle 0.54299 (40969) SS BOND : bond 0.00249 ( 63) SS BOND : angle 0.76168 ( 126) hydrogen bonds : bond 0.04378 ( 1130) hydrogen bonds : angle 4.79710 ( 3147) link_BETA1-4 : bond 0.00342 ( 15) link_BETA1-4 : angle 1.33804 ( 45) link_NAG-ASN : bond 0.00257 ( 41) link_NAG-ASN : angle 1.64564 ( 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 152 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7662 (mt0) cc_final: 0.7309 (mp10) REVERT: J 389 ILE cc_start: 0.8915 (mm) cc_final: 0.8699 (tt) REVERT: A 122 MET cc_start: 0.8105 (tpp) cc_final: 0.7730 (tpp) REVERT: A 1057 GLN cc_start: 0.8871 (mt0) cc_final: 0.8655 (tm-30) REVERT: B 723 ILE cc_start: 0.9451 (mp) cc_final: 0.9218 (mt) REVERT: B 859 GLU cc_start: 0.8647 (tp30) cc_final: 0.8388 (tt0) outliers start: 39 outliers final: 30 residues processed: 151 average time/residue: 0.1603 time to fit residues: 42.3290 Evaluate side-chains 132 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 270 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 856 GLU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 282 optimal weight: 0.3980 chunk 168 optimal weight: 0.9990 chunk 367 optimal weight: 40.0000 chunk 205 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 318 optimal weight: 0.2980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 157 ASN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 865 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.052476 restraints weight = 83374.797| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.98 r_work: 0.2625 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30202 Z= 0.103 Angle : 0.514 14.912 41263 Z= 0.268 Chirality : 0.042 0.207 4817 Planarity : 0.004 0.047 5229 Dihedral : 5.201 54.172 5254 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 6.49 % Favored : 92.51 % 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: 1.83 (0.20), residues: 791 sheet: 0.54 (0.18), residues: 776 loop : -0.33 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 944 TYR 0.012 0.001 TYR A 79 PHE 0.028 0.001 PHE B 268 TRP 0.016 0.001 TRP J 192 HIS 0.012 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00222 (30083) covalent geometry : angle 0.50589 (40969) SS BOND : bond 0.00172 ( 63) SS BOND : angle 0.59149 ( 126) hydrogen bonds : bond 0.03960 ( 1130) hydrogen bonds : angle 4.63938 ( 3147) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.30724 ( 45) link_NAG-ASN : bond 0.00280 ( 41) link_NAG-ASN : angle 1.58082 ( 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 146 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7632 (mt0) cc_final: 0.7298 (mp10) REVERT: J 1072 GLU cc_start: 0.8609 (tt0) cc_final: 0.8288 (tp30) REVERT: A 122 MET cc_start: 0.8089 (tpp) cc_final: 0.7737 (tpp) REVERT: B 723 ILE cc_start: 0.9430 (mp) cc_final: 0.9189 (mt) REVERT: B 859 GLU cc_start: 0.8633 (tp30) cc_final: 0.8362 (tt0) REVERT: B 1072 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8488 (mp0) outliers start: 31 outliers final: 24 residues processed: 145 average time/residue: 0.1705 time to fit residues: 42.4979 Evaluate side-chains 127 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 856 GLU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1072 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 59 optimal weight: 5.9990 chunk 371 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 227 optimal weight: 0.0870 chunk 285 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 306 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051845 restraints weight = 83808.145| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.98 r_work: 0.2608 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30202 Z= 0.137 Angle : 0.529 15.262 41263 Z= 0.274 Chirality : 0.042 0.229 4817 Planarity : 0.004 0.050 5229 Dihedral : 5.212 54.768 5254 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.07 % Allowed : 6.68 % Favored : 92.25 % 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: 0.49 (0.14), residues: 3505 helix: 1.87 (0.20), residues: 781 sheet: 0.47 (0.18), residues: 786 loop : -0.35 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 944 TYR 0.012 0.001 TYR B 443 PHE 0.029 0.001 PHE B 268 TRP 0.012 0.001 TRP J 192 HIS 0.009 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00314 (30083) covalent geometry : angle 0.52141 (40969) SS BOND : bond 0.00231 ( 63) SS BOND : angle 0.60293 ( 126) hydrogen bonds : bond 0.04080 ( 1130) hydrogen bonds : angle 4.64634 ( 3147) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.30918 ( 45) link_NAG-ASN : bond 0.00257 ( 41) link_NAG-ASN : angle 1.57388 ( 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 135 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7750 (mt0) cc_final: 0.7451 (mp10) REVERT: J 389 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8799 (tt) REVERT: J 737 TYR cc_start: 0.7518 (m-80) cc_final: 0.7252 (m-10) REVERT: J 1072 GLU cc_start: 0.8607 (tt0) cc_final: 0.8296 (tp30) REVERT: A 122 MET cc_start: 0.8159 (tpp) cc_final: 0.7808 (tpp) REVERT: A 1029 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 723 ILE cc_start: 0.9441 (mp) cc_final: 0.9211 (mt) REVERT: B 859 GLU cc_start: 0.8585 (tp30) cc_final: 0.8299 (tt0) REVERT: B 943 ILE cc_start: 0.8654 (mm) cc_final: 0.8394 (mp) REVERT: B 1072 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8493 (mp0) outliers start: 33 outliers final: 27 residues processed: 133 average time/residue: 0.1742 time to fit residues: 39.8567 Evaluate side-chains 128 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 856 GLU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 246 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 370 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.065873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051100 restraints weight = 83245.707| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.95 r_work: 0.2580 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30202 Z= 0.181 Angle : 0.559 16.100 41263 Z= 0.289 Chirality : 0.043 0.216 4817 Planarity : 0.004 0.051 5229 Dihedral : 5.396 55.617 5254 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.10 % Allowed : 6.71 % Favored : 92.18 % 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: 0.39 (0.14), residues: 3505 helix: 1.81 (0.20), residues: 781 sheet: 0.40 (0.18), residues: 784 loop : -0.42 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.015 0.001 TYR B 443 PHE 0.030 0.001 PHE B 268 TRP 0.010 0.001 TRP B 460 HIS 0.009 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00422 (30083) covalent geometry : angle 0.55052 (40969) SS BOND : bond 0.00281 ( 63) SS BOND : angle 0.76583 ( 126) hydrogen bonds : bond 0.04381 ( 1130) hydrogen bonds : angle 4.75042 ( 3147) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.32743 ( 45) link_NAG-ASN : bond 0.00260 ( 41) link_NAG-ASN : angle 1.61908 ( 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 137 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 389 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8904 (tt) REVERT: J 737 TYR cc_start: 0.7556 (m-80) cc_final: 0.7290 (m-10) REVERT: J 1072 GLU cc_start: 0.8616 (tt0) cc_final: 0.8314 (tp30) REVERT: A 122 MET cc_start: 0.8203 (tpp) cc_final: 0.7831 (tpp) REVERT: B 723 ILE cc_start: 0.9489 (mp) cc_final: 0.9285 (mt) REVERT: B 859 GLU cc_start: 0.8672 (tp30) cc_final: 0.8383 (tt0) REVERT: B 943 ILE cc_start: 0.8730 (mm) cc_final: 0.8449 (mp) REVERT: B 1072 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8441 (mp0) outliers start: 34 outliers final: 31 residues processed: 134 average time/residue: 0.1705 time to fit residues: 39.5885 Evaluate side-chains 130 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 389 ILE Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 856 GLU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 43 optimal weight: 0.7980 chunk 315 optimal weight: 0.8980 chunk 347 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 249 optimal weight: 0.0030 chunk 367 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 363 optimal weight: 30.0000 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.051909 restraints weight = 82443.910| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.96 r_work: 0.2604 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30202 Z= 0.127 Angle : 0.523 15.327 41263 Z= 0.271 Chirality : 0.042 0.205 4817 Planarity : 0.004 0.051 5229 Dihedral : 5.237 54.974 5254 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.01 % Allowed : 6.88 % Favored : 92.12 % 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: 0.43 (0.14), residues: 3505 helix: 1.92 (0.20), residues: 775 sheet: 0.44 (0.18), residues: 781 loop : -0.43 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 944 TYR 0.012 0.001 TYR A 667 PHE 0.029 0.001 PHE B 268 TRP 0.013 0.001 TRP J 192 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00291 (30083) covalent geometry : angle 0.51468 (40969) SS BOND : bond 0.00215 ( 63) SS BOND : angle 0.62104 ( 126) hydrogen bonds : bond 0.04044 ( 1130) hydrogen bonds : angle 4.65146 ( 3147) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.30544 ( 45) link_NAG-ASN : bond 0.00262 ( 41) link_NAG-ASN : angle 1.55541 ( 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 139 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 737 TYR cc_start: 0.7559 (m-80) cc_final: 0.7320 (m-10) REVERT: J 1072 GLU cc_start: 0.8581 (tt0) cc_final: 0.8295 (tp30) REVERT: A 122 MET cc_start: 0.8235 (tpp) cc_final: 0.7853 (tpp) REVERT: B 723 ILE cc_start: 0.9464 (mp) cc_final: 0.9263 (mt) REVERT: B 859 GLU cc_start: 0.8627 (tp30) cc_final: 0.8339 (tt0) REVERT: B 943 ILE cc_start: 0.8723 (mm) cc_final: 0.8426 (mp) REVERT: B 1072 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8412 (mp0) outliers start: 31 outliers final: 29 residues processed: 136 average time/residue: 0.1658 time to fit residues: 39.4140 Evaluate side-chains 130 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 856 GLU Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 294 optimal weight: 1.9990 chunk 292 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 360 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 269 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1138 ASN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.049832 restraints weight = 83642.418| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.94 r_work: 0.2546 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 30202 Z= 0.261 Angle : 0.639 22.883 41263 Z= 0.328 Chirality : 0.045 0.261 4817 Planarity : 0.004 0.049 5229 Dihedral : 5.675 56.936 5254 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.14 % Allowed : 6.91 % Favored : 91.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3505 helix: 1.66 (0.20), residues: 782 sheet: 0.35 (0.18), residues: 802 loop : -0.56 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 944 TYR 0.016 0.002 TYR J 633 PHE 0.031 0.002 PHE B 268 TRP 0.009 0.001 TRP A 983 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00611 (30083) covalent geometry : angle 0.61725 (40969) SS BOND : bond 0.00402 ( 63) SS BOND : angle 2.53732 ( 126) hydrogen bonds : bond 0.04797 ( 1130) hydrogen bonds : angle 4.89130 ( 3147) link_BETA1-4 : bond 0.00278 ( 15) link_BETA1-4 : angle 1.35614 ( 45) link_NAG-ASN : bond 0.00319 ( 41) link_NAG-ASN : angle 1.72782 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.51 seconds wall clock time: 88 minutes 13.17 seconds (5293.17 seconds total)