Starting phenix.real_space_refine on Sun Jul 5 18:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb3_24968/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.map" model { file = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_2026/7sb3_24968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb3_24968/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 6.62, per 1000 atoms: 0.22 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: 2.70 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: 1.44 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: 8.46 Time building geometry restraints manager: 3.52 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 - 19.77: 16939 19.77 - 39.53: 361 39.53 - 59.30: 148 59.30 - 79.07: 26 79.07 - 98.84: 7 Dihedral angle restraints: 17481 sinusoidal: 6495 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 17478 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: 3.070 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.410 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 10.121 98.836 10248 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/Z covalent geometry : bond 0.01871 / 1.00 (30083) covalent geometry : angle 1.74267 / 1.16 (40969) SS BOND : bond 0.03341 / 1.77 ( 63) SS BOND : angle 2.48218 / 1.74 ( 126) hydrogen bonds : bond 0.16991 / 11.35 ( 1130) hydrogen bonds : angle 7.63430 / 5.38 ( 3147) link_BETA1-4 : bond 0.02830 / 1.76 ( 15) link_BETA1-4 : angle 3.49448 / 2.03 ( 45) link_NAG-ASN : bond 0.02882 / 1.86 ( 41) link_NAG-ASN : angle 2.29643 / 1.63 ( 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 : 1.189 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: 0.2045 time to fit residues: 126.0019 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 : 1.091 ------------------------------------------------------------------------------- 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... 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 663 ASN A 724 ASN A 849 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.056599 restraints weight = 84526.922| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.98 r_work: 0.2740 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30202 Z= 0.177 Angle : 0.700 16.369 41263 Z= 0.365 Chirality : 0.046 0.365 4817 Planarity : 0.004 0.048 5229 Dihedral : 6.191 70.841 4090 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.91 % Allowed : 4.28 % Favored : 94.81 % 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: 1.13 (0.19), residues: 790 sheet: 0.66 (0.17), residues: 797 loop : 0.14 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 944 TYR 0.018 0.002 TYR A 221 PHE 0.019 0.002 PHE A 286 TRP 0.021 0.002 TRP B 460 HIS 0.015 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (30083) covalent geometry : angle 0.68292 / 0.36 (40969) SS BOND : bond 0.00301 / 0.23 ( 63) SS BOND : angle 0.96147 / 0.66 ( 126) hydrogen bonds : bond 0.05866 / 3.83 ( 1130) hydrogen bonds : angle 5.67738 / 3.98 ( 3147) link_BETA1-4 : bond 0.00329 / 0.20 ( 15) link_BETA1-4 : angle 1.89092 / 1.26 ( 45) link_NAG-ASN : bond 0.00359 / 0.26 ( 41) link_NAG-ASN : angle 2.61572 / 1.85 ( 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 185 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7998 (tpp) cc_final: 0.7389 (tpp) REVERT: A 1138 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7640 (t0) REVERT: B 859 GLU cc_start: 0.8628 (tp30) cc_final: 0.8307 (tt0) outliers start: 28 outliers final: 16 residues processed: 180 average time/residue: 0.1843 time to fit residues: 55.6249 Evaluate side-chains 131 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 605 LEU 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 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 787 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 308 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 305 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 252 HIS J 388 ASN J 429 ASN J 444 ASN J 849 ASN J1000 ASN J1147 GLN A1103 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056144 restraints weight = 84461.823| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.02 r_work: 0.2728 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30202 Z= 0.120 Angle : 0.563 16.432 41263 Z= 0.295 Chirality : 0.043 0.268 4817 Planarity : 0.004 0.042 5229 Dihedral : 5.370 57.972 4080 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.17 % Allowed : 4.96 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3505 helix: 1.50 (0.19), residues: 795 sheet: 0.69 (0.17), residues: 781 loop : -0.00 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.014 0.001 TYR J 79 PHE 0.027 0.001 PHE B 268 TRP 0.014 0.001 TRP J 192 HIS 0.009 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (30083) covalent geometry : angle 0.55200 / 0.29 (40969) SS BOND : bond 0.00221 / 0.18 ( 63) SS BOND : angle 0.79416 / 0.50 ( 126) hydrogen bonds : bond 0.04633 / 3.04 ( 1130) hydrogen bonds : angle 5.07502 / 3.54 ( 3147) link_BETA1-4 : bond 0.00416 / 0.25 ( 15) link_BETA1-4 : angle 1.33141 / 0.89 ( 45) link_NAG-ASN : bond 0.00339 / 0.27 ( 41) link_NAG-ASN : angle 1.93021 / 1.19 ( 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 170 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7990 (m-80) cc_final: 0.7625 (m-80) REVERT: A 122 MET cc_start: 0.7956 (tpp) cc_final: 0.7254 (tpp) REVERT: A 191 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8921 (tp) REVERT: B 595 ASP cc_start: 0.8470 (t0) cc_final: 0.8266 (t0) REVERT: B 859 GLU cc_start: 0.8510 (tp30) cc_final: 0.8256 (tt0) outliers start: 36 outliers final: 17 residues processed: 165 average time/residue: 0.1646 time to fit residues: 47.8281 Evaluate side-chains 125 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.0670 chunk 87 optimal weight: 1.9990 chunk 356 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 328 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 719 GLN J1011 GLN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 533 ASN A 874 ASN A 996 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051603 restraints weight = 84449.684| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.01 r_work: 0.2604 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30202 Z= 0.192 Angle : 0.608 17.431 41263 Z= 0.315 Chirality : 0.044 0.184 4817 Planarity : 0.004 0.045 5229 Dihedral : 5.341 57.380 4080 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.04 % Allowed : 5.38 % Favored : 93.58 % 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: 0.58 (0.14), residues: 3505 helix: 1.60 (0.19), residues: 782 sheet: 0.57 (0.18), residues: 789 loop : -0.14 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 80 TYR 0.017 0.002 TYR J 282 PHE 0.027 0.002 PHE B 268 TRP 0.009 0.001 TRP B 460 HIS 0.023 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (30083) covalent geometry : angle 0.59904 / 0.31 (40969) SS BOND : bond 0.00342 / 0.27 ( 63) SS BOND : angle 0.78953 / 0.52 ( 126) hydrogen bonds : bond 0.04839 / 3.20 ( 1130) hydrogen bonds : angle 5.02991 / 3.50 ( 3147) link_BETA1-4 : bond 0.00372 / 0.22 ( 15) link_BETA1-4 : angle 1.34844 / 0.89 ( 45) link_NAG-ASN : bond 0.00315 / 0.22 ( 41) link_NAG-ASN : angle 1.77507 / 1.12 ( 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 150 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8098 (tpp) cc_final: 0.7600 (tpp) REVERT: B 595 ASP cc_start: 0.8506 (t0) cc_final: 0.8284 (t0) REVERT: B 810 MET cc_start: 0.8850 (ttp) cc_final: 0.8636 (ttm) REVERT: B 859 GLU cc_start: 0.8598 (tp30) cc_final: 0.8168 (tt0) REVERT: B 1006 MET cc_start: 0.9218 (mmm) cc_final: 0.8955 (tpp) outliers start: 32 outliers final: 24 residues processed: 147 average time/residue: 0.1754 time to fit residues: 44.4578 Evaluate side-chains 128 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 142 VAL 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 787 ASN Chi-restraints excluded: chain J residue 810 MET 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 J residue 1078 ASP Chi-restraints excluded: chain A residue 311 GLN 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 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 353 SER 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 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: 0.6980 chunk 239 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 269 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 332 optimal weight: 0.5980 chunk 251 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** 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 = 0.3138 r_free = 0.3138 target = 0.068474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.053517 restraints weight = 83816.727| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.01 r_work: 0.2655 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30202 Z= 0.100 Angle : 0.516 14.990 41263 Z= 0.270 Chirality : 0.042 0.195 4817 Planarity : 0.004 0.046 5229 Dihedral : 4.938 48.250 4080 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 6.03 % Favored : 93.09 % 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: 1.80 (0.20), residues: 784 sheet: 0.65 (0.18), residues: 777 loop : -0.19 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 944 TYR 0.016 0.001 TYR A 79 PHE 0.026 0.001 PHE B 268 TRP 0.019 0.001 TRP J 192 HIS 0.018 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (30083) covalent geometry : angle 0.50759 / 0.27 (40969) SS BOND : bond 0.00206 / 0.17 ( 63) SS BOND : angle 0.62426 / 0.42 ( 126) hydrogen bonds : bond 0.04025 / 2.65 ( 1130) hydrogen bonds : angle 4.74114 / 3.30 ( 3147) link_BETA1-4 : bond 0.00400 / 0.24 ( 15) link_BETA1-4 : angle 1.21130 / 0.83 ( 45) link_NAG-ASN : bond 0.00308 / 0.23 ( 41) link_NAG-ASN : angle 1.60210 / 0.98 ( 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 146 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7463 (mt0) cc_final: 0.7112 (mp10) REVERT: A 117 PHE cc_start: 0.7977 (m-80) cc_final: 0.7733 (m-80) REVERT: A 122 MET cc_start: 0.8028 (tpp) cc_final: 0.7604 (tpp) REVERT: A 191 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 1057 GLN cc_start: 0.8784 (mt0) cc_final: 0.8543 (tm-30) REVERT: B 859 GLU cc_start: 0.8600 (tp30) cc_final: 0.8327 (tt0) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.1710 time to fit residues: 43.0175 Evaluate side-chains 128 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 333 VAL 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 1066 ILE Chi-restraints excluded: chain A residue 191 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 422 LEU 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: 4.9990 chunk 326 optimal weight: 10.0000 chunk 356 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 361 optimal weight: 20.0000 chunk 335 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 609 ASN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN B 874 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.049668 restraints weight = 84331.991| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.98 r_work: 0.2550 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 30202 Z= 0.275 Angle : 0.640 17.374 41263 Z= 0.330 Chirality : 0.045 0.198 4817 Planarity : 0.004 0.049 5229 Dihedral : 5.348 52.717 4080 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.30 % Allowed : 6.23 % Favored : 92.47 % 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: 0.34 (0.14), residues: 3505 helix: 1.54 (0.20), residues: 788 sheet: 0.41 (0.17), residues: 805 loop : -0.37 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 944 TYR 0.018 0.002 TYR A 79 PHE 0.030 0.002 PHE B 268 TRP 0.009 0.002 TRP B 460 HIS 0.012 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (30083) covalent geometry : angle 0.63064 / 0.33 (40969) SS BOND : bond 0.00354 / 0.26 ( 63) SS BOND : angle 0.93504 / 0.60 ( 126) hydrogen bonds : bond 0.05050 / 3.35 ( 1130) hydrogen bonds : angle 5.03225 / 3.49 ( 3147) link_BETA1-4 : bond 0.00293 / 0.17 ( 15) link_BETA1-4 : angle 1.34252 / 0.86 ( 45) link_NAG-ASN : bond 0.00364 / 0.25 ( 41) link_NAG-ASN : angle 1.79726 / 1.16 ( 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 151 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7770 (mt0) cc_final: 0.7383 (mp10) REVERT: A 122 MET cc_start: 0.8067 (tpp) cc_final: 0.7682 (tpp) REVERT: A 862 ASP cc_start: 0.8801 (p0) cc_final: 0.8594 (p0) REVERT: A 1057 GLN cc_start: 0.8920 (mt0) cc_final: 0.8657 (tm-30) REVERT: B 264 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7487 (pmt170) REVERT: B 698 GLU cc_start: 0.8875 (pt0) cc_final: 0.8652 (pm20) REVERT: B 859 GLU cc_start: 0.8677 (tp30) cc_final: 0.8417 (tt0) outliers start: 40 outliers final: 29 residues processed: 148 average time/residue: 0.1653 time to fit residues: 41.9019 Evaluate side-chains 126 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain J residue 142 VAL 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 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 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain J residue 1166 VAL Chi-restraints excluded: chain A residue 311 GLN 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 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1217 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 0.0870 chunk 282 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 367 optimal weight: 30.0000 chunk 205 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 318 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 157 ASN J 800 GLN ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN B 867 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051466 restraints weight = 83661.781| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.99 r_work: 0.2595 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30202 Z= 0.123 Angle : 0.535 15.979 41263 Z= 0.279 Chirality : 0.042 0.189 4817 Planarity : 0.004 0.046 5229 Dihedral : 5.042 51.173 4080 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.04 % Allowed : 6.58 % Favored : 92.38 % 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: 0.41 (0.14), residues: 3505 helix: 1.80 (0.20), residues: 779 sheet: 0.40 (0.18), residues: 787 loop : -0.38 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 944 TYR 0.013 0.001 TYR B 443 PHE 0.019 0.001 PHE A 286 TRP 0.015 0.001 TRP J 192 HIS 0.011 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (30083) covalent geometry : angle 0.52719 / 0.28 (40969) SS BOND : bond 0.00194 / 0.15 ( 63) SS BOND : angle 0.67040 / 0.44 ( 126) hydrogen bonds : bond 0.04259 / 2.82 ( 1130) hydrogen bonds : angle 4.79966 / 3.33 ( 3147) link_BETA1-4 : bond 0.00344 / 0.21 ( 15) link_BETA1-4 : angle 1.22397 / 0.83 ( 45) link_NAG-ASN : bond 0.00255 / 0.19 ( 41) link_NAG-ASN : angle 1.57987 / 0.99 ( 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 140 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 160 GLN cc_start: 0.7695 (mt0) cc_final: 0.7354 (mp10) REVERT: A 117 PHE cc_start: 0.8060 (m-80) cc_final: 0.7858 (m-80) REVERT: A 122 MET cc_start: 0.8096 (tpp) cc_final: 0.7721 (tpp) REVERT: A 191 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 717 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 1057 GLN cc_start: 0.8881 (mt0) cc_final: 0.8657 (tm-30) REVERT: B 698 GLU cc_start: 0.8862 (pt0) cc_final: 0.8616 (pm20) REVERT: B 723 ILE cc_start: 0.9456 (mp) cc_final: 0.9204 (mt) REVERT: B 859 GLU cc_start: 0.8587 (tp30) cc_final: 0.8290 (tt0) outliers start: 32 outliers final: 26 residues processed: 138 average time/residue: 0.1713 time to fit residues: 40.8577 Evaluate side-chains 126 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU 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 191 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 717 ILE 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 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1217 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 59 optimal weight: 4.9990 chunk 371 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3074 r_free = 0.3074 target = 0.065678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.050817 restraints weight = 83015.222| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.95 r_work: 0.2577 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30202 Z= 0.175 Angle : 0.561 16.208 41263 Z= 0.291 Chirality : 0.043 0.190 4817 Planarity : 0.004 0.047 5229 Dihedral : 5.068 52.412 4080 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.32 (0.14), residues: 3505 helix: 1.68 (0.20), residues: 786 sheet: 0.37 (0.17), residues: 799 loop : -0.45 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 944 TYR 0.014 0.001 TYR B 443 PHE 0.028 0.001 PHE B 268 TRP 0.011 0.001 TRP B 460 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (30083) covalent geometry : angle 0.55348 / 0.29 (40969) SS BOND : bond 0.00351 / 0.29 ( 63) SS BOND : angle 0.68000 / 0.45 ( 126) hydrogen bonds : bond 0.04431 / 2.94 ( 1130) hydrogen bonds : angle 4.80714 / 3.33 ( 3147) link_BETA1-4 : bond 0.00299 / 0.17 ( 15) link_BETA1-4 : angle 1.25914 / 0.83 ( 45) link_NAG-ASN : bond 0.00270 / 0.20 ( 41) link_NAG-ASN : angle 1.62181 / 1.03 ( 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 137 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8160 (tpp) cc_final: 0.7777 (tpp) REVERT: A 717 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8838 (mm) REVERT: A 1057 GLN cc_start: 0.8908 (mt0) cc_final: 0.8660 (tm-30) REVERT: B 698 GLU cc_start: 0.8932 (pt0) cc_final: 0.8638 (pm20) REVERT: B 723 ILE cc_start: 0.9492 (mp) cc_final: 0.9252 (mt) REVERT: B 859 GLU cc_start: 0.8722 (tp30) cc_final: 0.8431 (tt0) outliers start: 34 outliers final: 27 residues processed: 134 average time/residue: 0.1715 time to fit residues: 40.0483 Evaluate side-chains 126 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 219 HIS 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 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 717 ILE 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 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1217 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 246 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 370 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 313 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.050898 restraints weight = 83157.689| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.95 r_work: 0.2580 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30202 Z= 0.165 Angle : 0.551 16.103 41263 Z= 0.285 Chirality : 0.043 0.190 4817 Planarity : 0.004 0.047 5229 Dihedral : 5.018 52.344 4080 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.04 % Allowed : 7.01 % Favored : 91.96 % 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: 0.29 (0.14), residues: 3505 helix: 1.69 (0.20), residues: 787 sheet: 0.37 (0.18), residues: 784 loop : -0.49 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 944 TYR 0.014 0.001 TYR B 443 PHE 0.034 0.001 PHE B 268 TRP 0.013 0.001 TRP B 460 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (30083) covalent geometry : angle 0.54323 / 0.28 (40969) SS BOND : bond 0.00269 / 0.21 ( 63) SS BOND : angle 0.71768 / 0.47 ( 126) hydrogen bonds : bond 0.04341 / 2.88 ( 1130) hydrogen bonds : angle 4.77866 / 3.31 ( 3147) link_BETA1-4 : bond 0.00306 / 0.18 ( 15) link_BETA1-4 : angle 1.25111 / 0.84 ( 45) link_NAG-ASN : bond 0.00250 / 0.19 ( 41) link_NAG-ASN : angle 1.58423 / 1.01 ( 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 133 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 737 TYR cc_start: 0.7513 (m-80) cc_final: 0.7307 (m-10) REVERT: A 122 MET cc_start: 0.8182 (tpp) cc_final: 0.7815 (tpp) REVERT: A 1057 GLN cc_start: 0.8911 (mt0) cc_final: 0.8656 (tm-30) REVERT: B 698 GLU cc_start: 0.8917 (pt0) cc_final: 0.8552 (pm20) REVERT: B 723 ILE cc_start: 0.9494 (mp) cc_final: 0.9261 (mt) REVERT: B 859 GLU cc_start: 0.8698 (tp30) cc_final: 0.8400 (tt0) outliers start: 32 outliers final: 29 residues processed: 130 average time/residue: 0.1595 time to fit residues: 36.4649 Evaluate side-chains 125 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 219 HIS 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 353 SER Chi-restraints excluded: chain B residue 422 LEU 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 1217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 43 optimal weight: 0.0770 chunk 315 optimal weight: 0.8980 chunk 347 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 249 optimal weight: 0.4980 chunk 367 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A1000 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051838 restraints weight = 82193.507| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.94 r_work: 0.2604 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4567 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= 0.125 Angle : 0.525 15.400 41263 Z= 0.272 Chirality : 0.042 0.184 4817 Planarity : 0.004 0.047 5229 Dihedral : 4.852 51.474 4080 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.91 % Allowed : 7.30 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3505 helix: 1.82 (0.20), residues: 781 sheet: 0.41 (0.18), residues: 782 loop : -0.49 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 944 TYR 0.012 0.001 TYR A 667 PHE 0.033 0.001 PHE B 268 TRP 0.014 0.001 TRP J 192 HIS 0.008 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (30083) covalent geometry : angle 0.51724 / 0.27 (40969) SS BOND : bond 0.00211 / 0.16 ( 63) SS BOND : angle 0.63777 / 0.42 ( 126) hydrogen bonds : bond 0.04040 / 2.68 ( 1130) hydrogen bonds : angle 4.67095 / 3.24 ( 3147) link_BETA1-4 : bond 0.00333 / 0.20 ( 15) link_BETA1-4 : angle 1.24152 / 0.84 ( 45) link_NAG-ASN : bond 0.00249 / 0.19 ( 41) link_NAG-ASN : angle 1.52462 / 0.96 ( 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 133 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 873 MET cc_start: 0.8826 (mmt) cc_final: 0.8535 (tpp) REVERT: J 1072 GLU cc_start: 0.8579 (tt0) cc_final: 0.8305 (tp30) REVERT: A 122 MET cc_start: 0.8202 (tpp) cc_final: 0.7869 (tpp) REVERT: A 1057 GLN cc_start: 0.8893 (mt0) cc_final: 0.8659 (tm-30) REVERT: B 698 GLU cc_start: 0.8890 (pt0) cc_final: 0.8352 (pp20) REVERT: B 723 ILE cc_start: 0.9475 (mp) cc_final: 0.9241 (mt) REVERT: B 859 GLU cc_start: 0.8715 (tp30) cc_final: 0.8439 (tt0) outliers start: 28 outliers final: 26 residues processed: 132 average time/residue: 0.1541 time to fit residues: 35.5812 Evaluate side-chains 127 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1066 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 294 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 360 optimal weight: 40.0000 chunk 171 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 316 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3034 r_free = 0.3034 target = 0.063917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049168 restraints weight = 83997.162| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.95 r_work: 0.2531 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 30202 Z= 0.298 Angle : 0.668 19.612 41263 Z= 0.342 Chirality : 0.046 0.281 4817 Planarity : 0.004 0.048 5229 Dihedral : 5.305 53.844 4080 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.17 % Allowed : 7.30 % Favored : 91.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.11 (0.14), residues: 3505 helix: 1.53 (0.20), residues: 784 sheet: 0.34 (0.18), residues: 797 loop : -0.65 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1093 TYR 0.018 0.002 TYR A 71 PHE 0.033 0.002 PHE B 268 TRP 0.011 0.002 TRP A 983 HIS 0.007 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.30 (30083) covalent geometry : angle 0.64935 / 0.34 (40969) SS BOND : bond 0.00397 / 0.29 ( 63) SS BOND : angle 2.28982 / 1.31 ( 126) hydrogen bonds : bond 0.05025 / 3.34 ( 1130) hydrogen bonds : angle 4.98526 / 3.44 ( 3147) link_BETA1-4 : bond 0.00284 / 0.17 ( 15) link_BETA1-4 : angle 1.34607 / 0.85 ( 45) link_NAG-ASN : bond 0.00379 / 0.26 ( 41) link_NAG-ASN : angle 1.78262 / 1.17 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4757.70 seconds wall clock time: 83 minutes 10.42 seconds (4990.42 seconds total)