Starting phenix.real_space_refine on Fri Mar 6 06:43:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx6_30897/03_2026/7dx6_30897.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18475 2.51 5 N 4720 2.21 5 O 5717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29045 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.51, per 1000 atoms: 0.22 Number of scatterers: 29045 At special positions: 0 Unit cell: (138.049, 195.66, 203.269, 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 133 16.00 O 5717 8.00 N 4720 7.00 C 18475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.85 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.52 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.17 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.11 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.87 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.31 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN D 90 " " NAG c 1 " - " ASN D 103 " " NAG d 1 " - " ASN D 432 " " NAG e 1 " - " ASN D 546 " Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.3 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6658 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 45 sheets defined 31.3% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.527A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.550A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.592A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.578A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.547A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.712A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.855A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.059A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.580A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.872A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.271A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3054 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: 5.79 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6680 1.33 - 1.45: 7463 1.45 - 1.58: 15368 1.58 - 1.70: 0 1.70 - 1.83: 181 Bond restraints: 29692 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.30e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.82e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" N PRO D 346 " pdb=" CD PRO D 346 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 29687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 39320 2.67 - 5.33: 972 5.33 - 8.00: 72 8.00 - 10.67: 9 10.67 - 13.34: 5 Bond angle restraints: 40378 Sorted by residual: angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.35 -9.59 1.59e+00 3.96e-01 3.63e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N THR C 315 " pdb=" CA THR C 315 " pdb=" C THR C 315 " ideal model delta sigma weight residual 111.24 117.64 -6.40 1.29e+00 6.01e-01 2.46e+01 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16183 17.94 - 35.88: 1755 35.88 - 53.82: 561 53.82 - 71.76: 184 71.76 - 89.70: 53 Dihedral angle restraints: 18736 sinusoidal: 8408 harmonic: 10328 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 18733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4768 0.330 - 0.660: 3 0.660 - 0.990: 5 0.990 - 1.320: 0 1.320 - 1.651: 1 Chirality restraints: 4777 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.81e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 4774 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG c 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" C7 NAG c 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.099 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN B 331 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.227 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.145 2.00e-02 2.50e+03 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 249 2.53 - 3.12: 21280 3.12 - 3.71: 41441 3.71 - 4.31: 62824 4.31 - 4.90: 103717 Nonbonded interactions: 229511 Sorted by model distance: nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.983 3.120 nonbonded pdb=" O SER C 316 " pdb=" ND2 ASN C 317 " model vdw 2.059 3.120 ... (remaining 229506 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 27 through 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 26.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.013 0.818 29814 Z= 0.585 Angle : 1.293 71.320 40704 Z= 0.673 Chirality : 0.073 1.651 4777 Planarity : 0.009 0.305 5112 Dihedral : 17.486 89.696 11958 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.24 % Favored : 88.49 % Rotamer: Outliers : 10.72 % Allowed : 15.93 % Favored : 73.35 % 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: -4.35 (0.11), residues: 3484 helix: -2.96 (0.12), residues: 1000 sheet: -2.03 (0.17), residues: 755 loop : -3.27 (0.12), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP C 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01129 (29692) covalent geometry : angle 1.00755 (40378) SS BOND : bond 0.16599 ( 40) SS BOND : angle 13.85045 ( 80) hydrogen bonds : bond 0.22478 ( 1075) hydrogen bonds : angle 8.11377 ( 3054) link_BETA1-4 : bond 0.03731 ( 28) link_BETA1-4 : angle 4.22337 ( 84) link_NAG-ASN : bond 0.02607 ( 54) link_NAG-ASN : angle 7.92752 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 333 poor density : 418 time to evaluate : 1.064 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6411 (t0) REVERT: A 153 MET cc_start: 0.0457 (mpp) cc_final: -0.0800 (ptt) REVERT: A 324 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: A 517 LEU cc_start: 0.4674 (OUTLIER) cc_final: 0.4303 (tt) REVERT: A 544 ASN cc_start: 0.8044 (p0) cc_final: 0.7568 (t0) REVERT: A 569 ILE cc_start: 0.8685 (mp) cc_final: 0.8062 (mt) REVERT: A 702 GLU cc_start: 0.4259 (OUTLIER) cc_final: 0.4056 (mm-30) REVERT: A 878 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 1029 MET cc_start: 0.9052 (tpp) cc_final: 0.8845 (tpp) REVERT: B 133 PHE cc_start: 0.6087 (m-80) cc_final: 0.5805 (m-80) REVERT: B 153 MET cc_start: 0.2259 (mpp) cc_final: -0.1231 (ptt) REVERT: B 335 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6150 (mt) REVERT: B 529 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7609 (mtpm) REVERT: C 153 MET cc_start: 0.2132 (mpp) cc_final: 0.1888 (mtm) REVERT: C 212 LEU cc_start: 0.5088 (tp) cc_final: 0.4254 (mt) REVERT: C 544 ASN cc_start: 0.7863 (p0) cc_final: 0.7588 (p0) REVERT: D 89 GLN cc_start: 0.2907 (mm110) cc_final: 0.2585 (pm20) REVERT: D 332 MET cc_start: 0.2508 (ttp) cc_final: 0.1684 (mpt) REVERT: D 338 ASN cc_start: 0.3067 (t0) cc_final: 0.2867 (m110) REVERT: D 345 HIS cc_start: 0.2863 (OUTLIER) cc_final: 0.2532 (p90) REVERT: D 474 MET cc_start: 0.2058 (mmm) cc_final: 0.1401 (mmt) REVERT: D 508 ASN cc_start: 0.1403 (m110) cc_final: 0.0061 (t0) REVERT: D 554 LEU cc_start: 0.3477 (tp) cc_final: 0.2776 (pp) REVERT: D 579 MET cc_start: 0.1379 (ptt) cc_final: 0.1114 (mtt) outliers start: 333 outliers final: 71 residues processed: 709 average time/residue: 0.5391 time to fit residues: 458.6237 Evaluate side-chains 278 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 345 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 188 ASN A 334 ASN A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 655 HIS A 751 ASN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1005 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 207 HIS B 422 ASN B 440 ASN B 498 GLN B 542 ASN B 644 GLN B 655 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 188 ASN C 207 HIS C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 607 GLN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS D 42 GLN D 58 ASN D 175 GLN D 195 HIS D 239 HIS D 277 ASN D 325 GLN D 378 HIS D 472 GLN D 505 HIS D 586 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.182425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120270 restraints weight = 47199.520| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.47 r_work: 0.2970 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29814 Z= 0.171 Angle : 0.791 13.713 40704 Z= 0.386 Chirality : 0.051 0.560 4777 Planarity : 0.006 0.065 5112 Dihedral : 9.598 59.987 5631 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.80 % Favored : 92.85 % Rotamer: Outliers : 5.63 % Allowed : 21.24 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.59 (0.13), residues: 3484 helix: -0.61 (0.16), residues: 988 sheet: -1.29 (0.18), residues: 717 loop : -2.61 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 518 TYR 0.019 0.002 TYR A 495 PHE 0.023 0.002 PHE D 28 TRP 0.021 0.002 TRP D 566 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00384 (29692) covalent geometry : angle 0.75446 (40378) SS BOND : bond 0.00570 ( 40) SS BOND : angle 1.91489 ( 80) hydrogen bonds : bond 0.05241 ( 1075) hydrogen bonds : angle 5.58992 ( 3054) link_BETA1-4 : bond 0.00716 ( 28) link_BETA1-4 : angle 2.36716 ( 84) link_NAG-ASN : bond 0.00411 ( 54) link_NAG-ASN : angle 3.24940 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 227 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0604 (mpp) cc_final: -0.2437 (tmt) REVERT: A 158 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4837 (mpp-170) REVERT: A 190 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6788 (mtt90) REVERT: A 238 PHE cc_start: 0.6803 (p90) cc_final: 0.6565 (p90) REVERT: A 324 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: A 544 ASN cc_start: 0.8682 (p0) cc_final: 0.7822 (t0) REVERT: A 591 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 856 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8309 (p0) REVERT: A 878 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 936 ASP cc_start: 0.7960 (m-30) cc_final: 0.7728 (m-30) REVERT: A 985 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7549 (p0) REVERT: A 988 GLU cc_start: 0.8099 (mp0) cc_final: 0.7453 (mp0) REVERT: A 1019 ARG cc_start: 0.8805 (tpt170) cc_final: 0.8432 (ttm110) REVERT: B 66 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5979 (t-90) REVERT: B 141 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6605 (pp) REVERT: B 153 MET cc_start: 0.0411 (mpp) cc_final: -0.2421 (ptp) REVERT: B 187 LYS cc_start: 0.6108 (mmpt) cc_final: 0.5898 (mtmt) REVERT: B 336 CYS cc_start: 0.5711 (OUTLIER) cc_final: 0.5389 (p) REVERT: B 437 ASN cc_start: 0.7025 (t0) cc_final: 0.6634 (p0) REVERT: B 529 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7240 (mtpm) REVERT: B 532 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (m-40) REVERT: B 534 VAL cc_start: 0.8699 (m) cc_final: 0.8493 (p) REVERT: B 740 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8809 (ttp) REVERT: B 985 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (p0) REVERT: C 53 ASP cc_start: 0.8117 (t70) cc_final: 0.7892 (t0) REVERT: C 141 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7476 (pt) REVERT: C 153 MET cc_start: 0.1627 (mpp) cc_final: 0.1413 (mtm) REVERT: C 195 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7678 (mtmt) REVERT: C 212 LEU cc_start: 0.5567 (tp) cc_final: 0.4666 (mp) REVERT: C 336 CYS cc_start: 0.3713 (OUTLIER) cc_final: 0.2907 (p) REVERT: C 740 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (ttm) REVERT: C 787 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8484 (mp10) REVERT: C 814 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8015 (mptp) REVERT: D 39 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6113 (tp) REVERT: D 72 PHE cc_start: 0.4647 (t80) cc_final: 0.4277 (m-10) REVERT: D 89 GLN cc_start: 0.3177 (mm110) cc_final: 0.2851 (pm20) REVERT: D 190 MET cc_start: 0.2808 (mtm) cc_final: 0.2235 (ttm) REVERT: D 230 PHE cc_start: 0.2457 (t80) cc_final: 0.2162 (t80) REVERT: D 231 GLU cc_start: 0.3153 (OUTLIER) cc_final: 0.2774 (mm-30) REVERT: D 332 MET cc_start: 0.3258 (ttp) cc_final: 0.1694 (mpt) REVERT: D 338 ASN cc_start: 0.3617 (t0) cc_final: 0.3288 (m-40) REVERT: D 341 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.2718 (mptt) REVERT: D 474 MET cc_start: 0.2122 (mmm) cc_final: 0.1499 (mmt) REVERT: D 504 PHE cc_start: 0.4393 (t80) cc_final: 0.4035 (p90) REVERT: D 508 ASN cc_start: 0.4191 (m110) cc_final: 0.2896 (t0) REVERT: D 556 ASN cc_start: 0.1452 (t0) cc_final: 0.1216 (m110) REVERT: D 579 MET cc_start: 0.0549 (ptt) cc_final: -0.0015 (mpp) outliers start: 175 outliers final: 70 residues processed: 382 average time/residue: 0.5390 time to fit residues: 248.0380 Evaluate side-chains 262 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 170 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 348 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 957 GLN A1005 GLN B 164 ASN B 564 GLN B 762 GLN C 49 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1010 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.179764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117137 restraints weight = 47128.658| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.32 r_work: 0.2925 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29814 Z= 0.223 Angle : 0.783 13.351 40704 Z= 0.375 Chirality : 0.052 0.573 4777 Planarity : 0.005 0.058 5112 Dihedral : 8.547 59.873 5558 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.54 % Rotamer: Outliers : 5.37 % Allowed : 21.85 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3484 helix: 0.14 (0.17), residues: 989 sheet: -1.10 (0.18), residues: 732 loop : -2.32 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 115 TYR 0.039 0.002 TYR D 521 PHE 0.023 0.002 PHE A 140 TRP 0.020 0.001 TRP D 566 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00535 (29692) covalent geometry : angle 0.74743 (40378) SS BOND : bond 0.00536 ( 40) SS BOND : angle 1.81540 ( 80) hydrogen bonds : bond 0.05239 ( 1075) hydrogen bonds : angle 5.37601 ( 3054) link_BETA1-4 : bond 0.00486 ( 28) link_BETA1-4 : angle 2.44474 ( 84) link_NAG-ASN : bond 0.00419 ( 54) link_NAG-ASN : angle 3.14868 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 194 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7614 (m110) cc_final: 0.7295 (p0) REVERT: A 131 CYS cc_start: 0.3884 (m) cc_final: 0.3401 (m) REVERT: A 153 MET cc_start: -0.0489 (mpp) cc_final: -0.2361 (tmt) REVERT: A 155 SER cc_start: 0.6500 (OUTLIER) cc_final: 0.6059 (p) REVERT: A 190 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6607 (mtt90) REVERT: A 198 ASP cc_start: 0.7449 (m-30) cc_final: 0.7239 (t0) REVERT: A 200 TYR cc_start: 0.8233 (m-80) cc_final: 0.7853 (m-80) REVERT: A 238 PHE cc_start: 0.6805 (p90) cc_final: 0.6554 (p90) REVERT: A 544 ASN cc_start: 0.8724 (p0) cc_final: 0.7717 (t0) REVERT: A 692 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 936 ASP cc_start: 0.7964 (m-30) cc_final: 0.7748 (m-30) REVERT: A 985 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7913 (p0) REVERT: B 66 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.6134 (t-90) REVERT: B 140 PHE cc_start: 0.8300 (p90) cc_final: 0.8041 (p90) REVERT: B 141 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6991 (pp) REVERT: B 153 MET cc_start: 0.0973 (mpp) cc_final: -0.1909 (ptp) REVERT: B 387 LEU cc_start: 0.8204 (mt) cc_final: 0.7857 (mp) REVERT: B 437 ASN cc_start: 0.6933 (t0) cc_final: 0.6731 (p0) REVERT: B 529 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7052 (mtpm) REVERT: B 740 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8824 (ttp) REVERT: C 141 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7453 (pt) REVERT: C 195 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: C 239 GLN cc_start: 0.7567 (tt0) cc_final: 0.7229 (mt0) REVERT: C 336 CYS cc_start: 0.4338 (OUTLIER) cc_final: 0.3428 (p) REVERT: C 740 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: C 787 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: C 1144 GLU cc_start: 0.8678 (tp30) cc_final: 0.8237 (tt0) REVERT: D 39 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.6005 (tp) REVERT: D 72 PHE cc_start: 0.4676 (t80) cc_final: 0.4424 (m-10) REVERT: D 89 GLN cc_start: 0.3506 (mm110) cc_final: 0.3098 (pm20) REVERT: D 131 LYS cc_start: 0.4191 (mttm) cc_final: 0.3939 (tmmt) REVERT: D 190 MET cc_start: 0.2707 (mtm) cc_final: 0.2228 (ttm) REVERT: D 233 ILE cc_start: -0.1013 (OUTLIER) cc_final: -0.1261 (tp) REVERT: D 332 MET cc_start: 0.2983 (ttp) cc_final: 0.1645 (mpt) REVERT: D 474 MET cc_start: 0.2178 (mmm) cc_final: 0.1646 (mmp) REVERT: D 504 PHE cc_start: 0.4453 (t80) cc_final: 0.4083 (p90) REVERT: D 508 ASN cc_start: 0.4096 (m110) cc_final: 0.3392 (t0) REVERT: D 556 ASN cc_start: 0.1498 (t0) cc_final: 0.1282 (m110) REVERT: D 579 MET cc_start: 0.0622 (ptt) cc_final: 0.0121 (mtp) outliers start: 167 outliers final: 70 residues processed: 337 average time/residue: 0.4772 time to fit residues: 197.2317 Evaluate side-chains 249 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 477 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 293 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 299 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 957 GLN B 164 ASN B1106 GLN C 115 GLN D 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120021 restraints weight = 46754.905| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.74 r_work: 0.2978 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29814 Z= 0.207 Angle : 0.749 12.082 40704 Z= 0.358 Chirality : 0.050 0.618 4777 Planarity : 0.004 0.058 5112 Dihedral : 7.953 59.407 5545 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.63 % Favored : 93.20 % Rotamer: Outliers : 5.25 % Allowed : 22.21 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3484 helix: 0.47 (0.17), residues: 980 sheet: -0.88 (0.18), residues: 753 loop : -2.17 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.054 0.002 TYR D 521 PHE 0.022 0.002 PHE A 140 TRP 0.018 0.001 TRP D 566 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00498 (29692) covalent geometry : angle 0.71761 (40378) SS BOND : bond 0.00608 ( 40) SS BOND : angle 2.02526 ( 80) hydrogen bonds : bond 0.04770 ( 1075) hydrogen bonds : angle 5.26602 ( 3054) link_BETA1-4 : bond 0.00492 ( 28) link_BETA1-4 : angle 2.32547 ( 84) link_NAG-ASN : bond 0.00384 ( 54) link_NAG-ASN : angle 2.79800 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 191 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7650 (m110) cc_final: 0.7370 (p0) REVERT: A 131 CYS cc_start: 0.3760 (m) cc_final: 0.3159 (m) REVERT: A 153 MET cc_start: 0.0153 (mpp) cc_final: -0.2203 (tmt) REVERT: A 188 ASN cc_start: 0.6084 (m-40) cc_final: 0.5608 (p0) REVERT: A 190 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6609 (mpt-90) REVERT: A 238 PHE cc_start: 0.6979 (p90) cc_final: 0.6709 (p90) REVERT: A 355 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4715 (ttt90) REVERT: A 544 ASN cc_start: 0.8720 (p0) cc_final: 0.7691 (t0) REVERT: A 692 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8919 (mm) REVERT: A 936 ASP cc_start: 0.7965 (m-30) cc_final: 0.7764 (m-30) REVERT: A 1142 GLN cc_start: 0.8446 (tp40) cc_final: 0.8135 (tm-30) REVERT: B 66 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6316 (t-90) REVERT: B 140 PHE cc_start: 0.8453 (p90) cc_final: 0.8235 (p90) REVERT: B 141 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7193 (pp) REVERT: B 153 MET cc_start: 0.1439 (mpp) cc_final: -0.1681 (ptp) REVERT: B 387 LEU cc_start: 0.8347 (mt) cc_final: 0.7950 (mp) REVERT: B 529 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6859 (mtpm) REVERT: B 654 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: B 740 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8816 (ttp) REVERT: C 141 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7795 (pt) REVERT: C 195 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7731 (mtmt) REVERT: C 239 GLN cc_start: 0.7753 (tt0) cc_final: 0.7409 (mt0) REVERT: C 336 CYS cc_start: 0.4134 (OUTLIER) cc_final: 0.3488 (p) REVERT: C 740 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8664 (ttm) REVERT: C 787 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: C 1144 GLU cc_start: 0.8663 (tp30) cc_final: 0.8296 (tt0) REVERT: D 81 GLN cc_start: 0.3320 (OUTLIER) cc_final: 0.2222 (tt0) REVERT: D 89 GLN cc_start: 0.3642 (mm110) cc_final: 0.3083 (pm20) REVERT: D 123 MET cc_start: -0.0687 (OUTLIER) cc_final: -0.1505 (ptm) REVERT: D 131 LYS cc_start: 0.4180 (mttm) cc_final: 0.3949 (tmmt) REVERT: D 190 MET cc_start: 0.2694 (mtm) cc_final: 0.2008 (ttm) REVERT: D 233 ILE cc_start: -0.0895 (OUTLIER) cc_final: -0.1139 (tp) REVERT: D 332 MET cc_start: 0.2647 (ttp) cc_final: 0.1564 (pmm) REVERT: D 504 PHE cc_start: 0.4257 (t80) cc_final: 0.3911 (p90) REVERT: D 508 ASN cc_start: 0.3456 (m110) cc_final: 0.2436 (t0) REVERT: D 555 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.4185 (p90) REVERT: D 579 MET cc_start: -0.0064 (ptt) cc_final: -0.0335 (mpp) outliers start: 163 outliers final: 73 residues processed: 332 average time/residue: 0.4918 time to fit residues: 198.9031 Evaluate side-chains 254 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 164 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 189 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 164 ASN B 239 GLN B1106 GLN C 207 HIS C 542 ASN ** D 24 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.178793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119111 restraints weight = 46840.248| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.86 r_work: 0.2963 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29814 Z= 0.204 Angle : 0.738 13.799 40704 Z= 0.351 Chirality : 0.050 0.598 4777 Planarity : 0.004 0.058 5112 Dihedral : 7.726 59.860 5543 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.28 % Rotamer: Outliers : 5.57 % Allowed : 21.95 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3484 helix: 0.58 (0.17), residues: 989 sheet: -0.72 (0.18), residues: 762 loop : -2.06 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.036 0.002 TYR D 521 PHE 0.019 0.002 PHE A 140 TRP 0.022 0.001 TRP D 566 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00492 (29692) covalent geometry : angle 0.70261 (40378) SS BOND : bond 0.00495 ( 40) SS BOND : angle 1.79958 ( 80) hydrogen bonds : bond 0.04651 ( 1075) hydrogen bonds : angle 5.24300 ( 3054) link_BETA1-4 : bond 0.00479 ( 28) link_BETA1-4 : angle 2.32617 ( 84) link_NAG-ASN : bond 0.00537 ( 54) link_NAG-ASN : angle 3.06559 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 175 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3779 (m) cc_final: 0.3157 (m) REVERT: A 153 MET cc_start: -0.0269 (mpp) cc_final: -0.2299 (tmt) REVERT: A 188 ASN cc_start: 0.6208 (m-40) cc_final: 0.5675 (p0) REVERT: A 190 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6613 (mpt-90) REVERT: A 238 PHE cc_start: 0.6997 (p90) cc_final: 0.6708 (p90) REVERT: A 355 ARG cc_start: 0.5042 (OUTLIER) cc_final: 0.4597 (ttt90) REVERT: A 544 ASN cc_start: 0.8676 (p0) cc_final: 0.7688 (t0) REVERT: A 692 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8911 (mm) REVERT: A 936 ASP cc_start: 0.8079 (m-30) cc_final: 0.7873 (m-30) REVERT: A 1142 GLN cc_start: 0.8433 (tp40) cc_final: 0.8105 (tm-30) REVERT: B 66 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6326 (t-90) REVERT: B 140 PHE cc_start: 0.8460 (p90) cc_final: 0.8163 (p90) REVERT: B 141 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7156 (pp) REVERT: B 153 MET cc_start: 0.1407 (mpp) cc_final: -0.1906 (ptp) REVERT: B 387 LEU cc_start: 0.8323 (mt) cc_final: 0.7925 (mp) REVERT: B 529 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6756 (mtpm) REVERT: B 740 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8844 (ttp) REVERT: C 141 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7711 (pt) REVERT: C 207 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.6930 (m170) REVERT: C 239 GLN cc_start: 0.7703 (tt0) cc_final: 0.7380 (mt0) REVERT: C 314 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8357 (tp40) REVERT: C 336 CYS cc_start: 0.4275 (OUTLIER) cc_final: 0.3380 (p) REVERT: C 740 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8680 (ttm) REVERT: C 787 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: C 1144 GLU cc_start: 0.8654 (tp30) cc_final: 0.8316 (tt0) REVERT: D 81 GLN cc_start: 0.3245 (OUTLIER) cc_final: 0.2168 (tt0) REVERT: D 89 GLN cc_start: 0.3552 (mm110) cc_final: 0.3149 (pm20) REVERT: D 190 MET cc_start: 0.2567 (mtm) cc_final: 0.2027 (ttm) REVERT: D 233 ILE cc_start: -0.0893 (OUTLIER) cc_final: -0.1156 (tp) REVERT: D 332 MET cc_start: 0.2559 (ttp) cc_final: 0.1628 (pmm) REVERT: D 504 PHE cc_start: 0.4381 (t80) cc_final: 0.3924 (p90) REVERT: D 508 ASN cc_start: 0.3518 (m110) cc_final: 0.2544 (t0) REVERT: D 587 TYR cc_start: 0.2486 (OUTLIER) cc_final: 0.2199 (t80) outliers start: 173 outliers final: 83 residues processed: 324 average time/residue: 0.4952 time to fit residues: 197.0548 Evaluate side-chains 264 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 165 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 587 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 202 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 164 ASN B 690 GLN C 207 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.178486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119556 restraints weight = 46784.651| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.85 r_work: 0.2966 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29814 Z= 0.202 Angle : 0.734 12.470 40704 Z= 0.348 Chirality : 0.050 0.584 4777 Planarity : 0.004 0.058 5112 Dihedral : 7.590 59.508 5536 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 5.05 % Allowed : 22.43 % Favored : 72.51 % Cbeta Deviations : 0.00 % 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: -1.31 (0.14), residues: 3484 helix: 0.70 (0.17), residues: 988 sheet: -0.63 (0.18), residues: 761 loop : -1.96 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.017 0.002 PHE A 86 TRP 0.025 0.002 TRP D 606 HIS 0.016 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00488 (29692) covalent geometry : angle 0.69823 (40378) SS BOND : bond 0.00463 ( 40) SS BOND : angle 1.78885 ( 80) hydrogen bonds : bond 0.04570 ( 1075) hydrogen bonds : angle 5.20120 ( 3054) link_BETA1-4 : bond 0.00476 ( 28) link_BETA1-4 : angle 2.27625 ( 84) link_NAG-ASN : bond 0.00379 ( 54) link_NAG-ASN : angle 3.07268 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 161 time to evaluate : 1.040 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: A 131 CYS cc_start: 0.3964 (m) cc_final: 0.3186 (m) REVERT: A 188 ASN cc_start: 0.6156 (m-40) cc_final: 0.5632 (p0) REVERT: A 190 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6544 (mpt-90) REVERT: A 216 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6335 (tt) REVERT: A 355 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4593 (ttt180) REVERT: A 544 ASN cc_start: 0.8652 (p0) cc_final: 0.7582 (t0) REVERT: A 692 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 936 ASP cc_start: 0.8133 (m-30) cc_final: 0.7929 (m-30) REVERT: A 1142 GLN cc_start: 0.8388 (tp40) cc_final: 0.8028 (tm-30) REVERT: B 66 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.6292 (t-90) REVERT: B 140 PHE cc_start: 0.8466 (p90) cc_final: 0.8130 (p90) REVERT: B 141 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7162 (pp) REVERT: B 153 MET cc_start: 0.1586 (mpp) cc_final: -0.1581 (ptp) REVERT: B 387 LEU cc_start: 0.8292 (mt) cc_final: 0.7897 (mp) REVERT: B 493 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: B 524 VAL cc_start: 0.6174 (OUTLIER) cc_final: 0.5900 (p) REVERT: B 654 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: B 740 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8856 (ttp) REVERT: C 141 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7833 (pt) REVERT: C 207 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.6857 (m170) REVERT: C 239 GLN cc_start: 0.7754 (tt0) cc_final: 0.7386 (mt0) REVERT: C 314 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: C 336 CYS cc_start: 0.4148 (OUTLIER) cc_final: 0.3386 (p) REVERT: C 740 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8699 (ttm) REVERT: C 787 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: D 69 TRP cc_start: 0.2613 (t-100) cc_final: 0.2404 (t60) REVERT: D 81 GLN cc_start: 0.3072 (OUTLIER) cc_final: 0.2305 (tt0) REVERT: D 89 GLN cc_start: 0.3571 (mm110) cc_final: 0.3206 (pm20) REVERT: D 123 MET cc_start: -0.0601 (OUTLIER) cc_final: -0.1406 (ptm) REVERT: D 190 MET cc_start: 0.2547 (mtm) cc_final: 0.1966 (ttm) REVERT: D 332 MET cc_start: 0.2720 (ttp) cc_final: 0.1043 (mpt) REVERT: D 504 PHE cc_start: 0.4264 (t80) cc_final: 0.3809 (p90) REVERT: D 508 ASN cc_start: 0.3409 (m110) cc_final: 0.2503 (t0) outliers start: 157 outliers final: 96 residues processed: 298 average time/residue: 0.4733 time to fit residues: 173.4929 Evaluate side-chains 265 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 151 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 76 optimal weight: 0.5980 chunk 266 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 339 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 325 optimal weight: 30.0000 chunk 264 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 580 GLN A 957 GLN B 164 ASN B 703 ASN C 207 HIS D 24 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120845 restraints weight = 47053.340| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.78 r_work: 0.3011 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29814 Z= 0.138 Angle : 0.692 10.959 40704 Z= 0.328 Chirality : 0.048 0.575 4777 Planarity : 0.004 0.055 5112 Dihedral : 7.195 59.322 5531 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 4.47 % Allowed : 22.82 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3484 helix: 0.88 (0.17), residues: 990 sheet: -0.45 (0.18), residues: 751 loop : -1.85 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE A 140 TRP 0.018 0.001 TRP D 477 HIS 0.015 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00320 (29692) covalent geometry : angle 0.65687 (40378) SS BOND : bond 0.00539 ( 40) SS BOND : angle 2.21148 ( 80) hydrogen bonds : bond 0.03937 ( 1075) hydrogen bonds : angle 5.05669 ( 3054) link_BETA1-4 : bond 0.00526 ( 28) link_BETA1-4 : angle 2.19812 ( 84) link_NAG-ASN : bond 0.00369 ( 54) link_NAG-ASN : angle 2.77193 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 170 time to evaluate : 1.072 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: A 95 THR cc_start: 0.7553 (p) cc_final: 0.7279 (t) REVERT: A 131 CYS cc_start: 0.3557 (m) cc_final: 0.2834 (m) REVERT: A 188 ASN cc_start: 0.6335 (m-40) cc_final: 0.5626 (p0) REVERT: A 190 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6514 (mpt-90) REVERT: A 347 PHE cc_start: 0.4591 (OUTLIER) cc_final: 0.4229 (t80) REVERT: A 355 ARG cc_start: 0.5302 (OUTLIER) cc_final: 0.4907 (ttt90) REVERT: A 544 ASN cc_start: 0.8641 (p0) cc_final: 0.7582 (t0) REVERT: A 646 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8607 (ttm-80) REVERT: A 692 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8878 (mm) REVERT: B 66 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.6186 (t-90) REVERT: B 140 PHE cc_start: 0.8420 (p90) cc_final: 0.8060 (p90) REVERT: B 153 MET cc_start: 0.1191 (mpp) cc_final: -0.2207 (ppp) REVERT: B 387 LEU cc_start: 0.8271 (mt) cc_final: 0.7891 (mp) REVERT: B 654 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: B 740 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8818 (ttp) REVERT: B 1092 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: C 141 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7825 (pt) REVERT: C 207 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6916 (m170) REVERT: C 239 GLN cc_start: 0.7703 (tt0) cc_final: 0.7404 (mt0) REVERT: C 336 CYS cc_start: 0.4001 (OUTLIER) cc_final: 0.3379 (p) REVERT: C 544 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7272 (p0) REVERT: C 740 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (ttm) REVERT: C 787 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: D 81 GLN cc_start: 0.3032 (OUTLIER) cc_final: 0.2275 (tt0) REVERT: D 89 GLN cc_start: 0.3543 (mm110) cc_final: 0.3204 (pm20) REVERT: D 123 MET cc_start: -0.0641 (OUTLIER) cc_final: -0.1414 (ptm) REVERT: D 190 MET cc_start: 0.2421 (mtm) cc_final: 0.1876 (ttm) REVERT: D 233 ILE cc_start: -0.0983 (OUTLIER) cc_final: -0.1241 (tp) REVERT: D 332 MET cc_start: 0.2635 (ttp) cc_final: 0.0987 (mpt) REVERT: D 504 PHE cc_start: 0.4211 (t80) cc_final: 0.3784 (p90) REVERT: D 508 ASN cc_start: 0.3382 (m110) cc_final: 0.2520 (t0) outliers start: 139 outliers final: 79 residues processed: 293 average time/residue: 0.5136 time to fit residues: 183.1100 Evaluate side-chains 252 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 156 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 442 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 188 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 chunk 347 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 191 optimal weight: 0.4980 chunk 222 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 957 GLN B 164 ASN C 207 HIS C1142 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117673 restraints weight = 46859.916| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.26 r_work: 0.2936 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29814 Z= 0.171 Angle : 0.706 11.482 40704 Z= 0.335 Chirality : 0.048 0.566 4777 Planarity : 0.004 0.057 5112 Dihedral : 7.044 59.594 5523 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.60 % Favored : 93.25 % Rotamer: Outliers : 4.28 % Allowed : 23.14 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3484 helix: 0.95 (0.17), residues: 991 sheet: -0.46 (0.18), residues: 755 loop : -1.79 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.021 0.001 PHE A 192 TRP 0.018 0.001 TRP D 477 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00411 (29692) covalent geometry : angle 0.67365 (40378) SS BOND : bond 0.00534 ( 40) SS BOND : angle 2.10968 ( 80) hydrogen bonds : bond 0.04228 ( 1075) hydrogen bonds : angle 5.07390 ( 3054) link_BETA1-4 : bond 0.00497 ( 28) link_BETA1-4 : angle 2.21135 ( 84) link_NAG-ASN : bond 0.00347 ( 54) link_NAG-ASN : angle 2.74567 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 160 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: A 131 CYS cc_start: 0.3583 (m) cc_final: 0.2827 (m) REVERT: A 188 ASN cc_start: 0.6160 (m-40) cc_final: 0.5603 (p0) REVERT: A 190 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6365 (mpt-90) REVERT: A 347 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.4107 (t80) REVERT: A 355 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.4561 (ttt180) REVERT: A 544 ASN cc_start: 0.8638 (p0) cc_final: 0.7542 (t0) REVERT: A 591 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 646 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8637 (ttm-80) REVERT: A 692 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 979 ASP cc_start: 0.8412 (m-30) cc_final: 0.8180 (t0) REVERT: A 1142 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8007 (tm-30) REVERT: B 66 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.6215 (t-90) REVERT: B 140 PHE cc_start: 0.8468 (p90) cc_final: 0.8041 (p90) REVERT: B 153 MET cc_start: 0.1287 (mpp) cc_final: -0.2051 (ppp) REVERT: B 654 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: B 900 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9184 (mtm) REVERT: B 1092 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: C 141 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (pt) REVERT: C 207 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6786 (m170) REVERT: C 239 GLN cc_start: 0.7632 (tt0) cc_final: 0.7337 (mt0) REVERT: C 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8383 (tp40) REVERT: C 336 CYS cc_start: 0.4913 (OUTLIER) cc_final: 0.3876 (p) REVERT: C 544 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7215 (p0) REVERT: C 740 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8671 (ttm) REVERT: C 787 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: D 48 TRP cc_start: 0.2871 (OUTLIER) cc_final: 0.2620 (m100) REVERT: D 81 GLN cc_start: 0.2521 (OUTLIER) cc_final: 0.2061 (tt0) REVERT: D 89 GLN cc_start: 0.3325 (mm110) cc_final: 0.2959 (pm20) REVERT: D 123 MET cc_start: -0.0653 (OUTLIER) cc_final: -0.1301 (ptm) REVERT: D 190 MET cc_start: 0.2358 (mtm) cc_final: 0.1907 (ttm) REVERT: D 233 ILE cc_start: -0.0750 (OUTLIER) cc_final: -0.1014 (tp) REVERT: D 332 MET cc_start: 0.3000 (ttp) cc_final: 0.1435 (mpt) REVERT: D 504 PHE cc_start: 0.4041 (t80) cc_final: 0.3625 (p90) REVERT: D 508 ASN cc_start: 0.3567 (m110) cc_final: 0.3030 (t0) REVERT: D 554 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1286 (tm) outliers start: 133 outliers final: 85 residues processed: 277 average time/residue: 0.5286 time to fit residues: 178.3728 Evaluate side-chains 258 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 152 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 0.8980 chunk 313 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 233 optimal weight: 30.0000 chunk 238 optimal weight: 7.9990 chunk 136 optimal weight: 0.0070 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 164 ASN C 207 HIS D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116369 restraints weight = 46593.243| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.65 r_work: 0.2945 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29814 Z= 0.190 Angle : 0.718 11.893 40704 Z= 0.342 Chirality : 0.049 0.571 4777 Planarity : 0.004 0.057 5112 Dihedral : 7.046 59.862 5523 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.80 % Favored : 93.03 % Rotamer: Outliers : 4.25 % Allowed : 23.40 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3484 helix: 0.91 (0.17), residues: 993 sheet: -0.46 (0.18), residues: 756 loop : -1.81 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.002 PHE D 523 TRP 0.019 0.001 TRP D 477 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00462 (29692) covalent geometry : angle 0.68671 (40378) SS BOND : bond 0.00518 ( 40) SS BOND : angle 1.99631 ( 80) hydrogen bonds : bond 0.04353 ( 1075) hydrogen bonds : angle 5.09498 ( 3054) link_BETA1-4 : bond 0.00493 ( 28) link_BETA1-4 : angle 2.22856 ( 84) link_NAG-ASN : bond 0.00362 ( 54) link_NAG-ASN : angle 2.76177 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 153 time to evaluate : 1.091 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: A 131 CYS cc_start: 0.3555 (m) cc_final: 0.2774 (m) REVERT: A 188 ASN cc_start: 0.6291 (m-40) cc_final: 0.5720 (p0) REVERT: A 190 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6438 (mpt-90) REVERT: A 347 PHE cc_start: 0.4282 (OUTLIER) cc_final: 0.3933 (t80) REVERT: A 355 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.4397 (ttt180) REVERT: A 544 ASN cc_start: 0.8629 (p0) cc_final: 0.7490 (t0) REVERT: A 591 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 646 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8671 (ttm-80) REVERT: A 692 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8862 (mm) REVERT: A 1005 GLN cc_start: 0.9061 (tt0) cc_final: 0.8810 (mt0) REVERT: A 1142 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8024 (tm-30) REVERT: B 66 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.6150 (t-90) REVERT: B 140 PHE cc_start: 0.8477 (p90) cc_final: 0.8032 (p90) REVERT: B 153 MET cc_start: 0.0945 (mpp) cc_final: -0.2486 (ppp) REVERT: B 335 LEU cc_start: 0.6791 (mp) cc_final: 0.6506 (tt) REVERT: B 654 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8533 (pt0) REVERT: B 900 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9166 (mtm) REVERT: B 1092 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: C 141 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7557 (pt) REVERT: C 207 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6768 (m170) REVERT: C 239 GLN cc_start: 0.7685 (tt0) cc_final: 0.7380 (mt0) REVERT: C 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8366 (tp40) REVERT: C 336 CYS cc_start: 0.4928 (OUTLIER) cc_final: 0.3861 (p) REVERT: C 544 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7229 (p0) REVERT: C 740 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (ttm) REVERT: C 787 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: D 48 TRP cc_start: 0.3008 (OUTLIER) cc_final: 0.2742 (m100) REVERT: D 81 GLN cc_start: 0.2456 (OUTLIER) cc_final: 0.2000 (tt0) REVERT: D 89 GLN cc_start: 0.3556 (mm110) cc_final: 0.3190 (pm20) REVERT: D 123 MET cc_start: -0.0625 (OUTLIER) cc_final: -0.1347 (ptm) REVERT: D 190 MET cc_start: 0.2389 (mtm) cc_final: 0.1916 (ttm) REVERT: D 233 ILE cc_start: -0.0812 (OUTLIER) cc_final: -0.1062 (tp) REVERT: D 332 MET cc_start: 0.2857 (ttp) cc_final: 0.1278 (mpt) REVERT: D 504 PHE cc_start: 0.4018 (t80) cc_final: 0.3598 (p90) REVERT: D 508 ASN cc_start: 0.3467 (m110) cc_final: 0.2768 (t0) outliers start: 132 outliers final: 91 residues processed: 269 average time/residue: 0.5160 time to fit residues: 170.7066 Evaluate side-chains 261 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 149 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 115 optimal weight: 8.9990 chunk 300 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 260 optimal weight: 0.7980 chunk 312 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 317 optimal weight: 0.0670 chunk 320 optimal weight: 0.0870 chunk 321 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C 207 HIS D 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.180484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121743 restraints weight = 46761.219| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.74 r_work: 0.3043 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29814 Z= 0.110 Angle : 0.666 10.291 40704 Z= 0.315 Chirality : 0.047 0.552 4777 Planarity : 0.004 0.054 5112 Dihedral : 6.635 59.097 5523 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 2.74 % Allowed : 24.91 % Favored : 72.35 % Cbeta Deviations : 0.00 % 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: -0.77 (0.14), residues: 3484 helix: 1.13 (0.17), residues: 996 sheet: -0.18 (0.19), residues: 745 loop : -1.69 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE D 523 TRP 0.024 0.001 TRP D 477 HIS 0.031 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (29692) covalent geometry : angle 0.63864 (40378) SS BOND : bond 0.00425 ( 40) SS BOND : angle 1.67959 ( 80) hydrogen bonds : bond 0.03374 ( 1075) hydrogen bonds : angle 4.85295 ( 3054) link_BETA1-4 : bond 0.00563 ( 28) link_BETA1-4 : angle 2.07735 ( 84) link_NAG-ASN : bond 0.00379 ( 54) link_NAG-ASN : angle 2.47217 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 171 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7545 (p) cc_final: 0.7265 (t) REVERT: A 131 CYS cc_start: 0.3512 (m) cc_final: 0.2819 (m) REVERT: A 188 ASN cc_start: 0.6318 (m-40) cc_final: 0.5680 (p0) REVERT: A 190 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6453 (mpt-90) REVERT: A 310 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8730 (ttpp) REVERT: A 355 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.4984 (ttt90) REVERT: A 544 ASN cc_start: 0.8651 (p0) cc_final: 0.7567 (t0) REVERT: A 646 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8644 (ttm-80) REVERT: A 770 ILE cc_start: 0.8574 (pt) cc_final: 0.8121 (mt) REVERT: A 935 GLN cc_start: 0.8646 (tt0) cc_final: 0.8326 (mt0) REVERT: A 1019 ARG cc_start: 0.8759 (tpt170) cc_final: 0.8514 (ttp-110) REVERT: A 1142 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8136 (tm-30) REVERT: B 66 HIS cc_start: 0.6279 (m-70) cc_final: 0.6017 (t-90) REVERT: B 140 PHE cc_start: 0.8477 (p90) cc_final: 0.8071 (p90) REVERT: B 153 MET cc_start: 0.1368 (mpp) cc_final: -0.2165 (ppp) REVERT: B 335 LEU cc_start: 0.6654 (mp) cc_final: 0.6394 (tt) REVERT: C 141 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7729 (pt) REVERT: C 239 GLN cc_start: 0.7778 (tt0) cc_final: 0.7474 (mt0) REVERT: C 336 CYS cc_start: 0.4484 (OUTLIER) cc_final: 0.3611 (p) REVERT: C 740 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (ttm) REVERT: C 787 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8567 (mp10) REVERT: C 1005 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8796 (mt0) REVERT: D 48 TRP cc_start: 0.3122 (OUTLIER) cc_final: 0.2791 (m100) REVERT: D 81 GLN cc_start: 0.2301 (OUTLIER) cc_final: 0.1823 (tt0) REVERT: D 89 GLN cc_start: 0.3435 (mm110) cc_final: 0.3077 (pm20) REVERT: D 123 MET cc_start: -0.0539 (OUTLIER) cc_final: -0.1294 (ptm) REVERT: D 190 MET cc_start: 0.2298 (mtm) cc_final: 0.1853 (ttm) REVERT: D 233 ILE cc_start: -0.1080 (OUTLIER) cc_final: -0.1307 (tp) REVERT: D 297 MET cc_start: -0.1371 (mmt) cc_final: -0.1626 (mmt) REVERT: D 332 MET cc_start: 0.2577 (ttp) cc_final: 0.1046 (mpt) REVERT: D 504 PHE cc_start: 0.3996 (t80) cc_final: 0.3585 (p90) REVERT: D 508 ASN cc_start: 0.3375 (m110) cc_final: 0.2627 (t0) outliers start: 85 outliers final: 53 residues processed: 246 average time/residue: 0.5647 time to fit residues: 167.4965 Evaluate side-chains 224 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 69 optimal weight: 0.0670 chunk 348 optimal weight: 6.9990 chunk 337 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 164 ASN C 207 HIS C 360 ASN C 613 GLN C 804 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118445 restraints weight = 46874.277| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.13 r_work: 0.2963 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29814 Z= 0.135 Angle : 0.681 10.409 40704 Z= 0.322 Chirality : 0.047 0.555 4777 Planarity : 0.004 0.056 5112 Dihedral : 6.583 58.771 5523 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 2.77 % Allowed : 25.01 % Favored : 72.22 % 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: -0.72 (0.14), residues: 3484 helix: 1.16 (0.17), residues: 998 sheet: -0.21 (0.19), residues: 755 loop : -1.63 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.018 0.001 TYR B1067 PHE 0.028 0.001 PHE D 523 TRP 0.024 0.001 TRP D 477 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (29692) covalent geometry : angle 0.65326 (40378) SS BOND : bond 0.00466 ( 40) SS BOND : angle 1.72746 ( 80) hydrogen bonds : bond 0.03759 ( 1075) hydrogen bonds : angle 4.87251 ( 3054) link_BETA1-4 : bond 0.00496 ( 28) link_BETA1-4 : angle 2.08737 ( 84) link_NAG-ASN : bond 0.00343 ( 54) link_NAG-ASN : angle 2.53523 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14050.77 seconds wall clock time: 238 minutes 27.53 seconds (14307.53 seconds total)