Starting phenix.real_space_refine on Fri Mar 6 06:44:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx5_30896/03_2026/7dx5_30896.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29045 Number of models: 1 Model: "" Number of chains: 34 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: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 6.74, per 1000 atoms: 0.23 Number of scatterers: 29045 At special positions: 0 Unit cell: (138.049, 193.486, 204.356, 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=2.17 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=2.56 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=2.03 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=2.12 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=2.12 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.44 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=2.12 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.45 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 B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " 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-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 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " 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 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN D 53 " " NAG a 1 " - " ASN D 90 " " NAG b 1 " - " ASN D 103 " " NAG c 1 " - " ASN D 432 " " NAG d 1 " - " ASN D 546 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 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 46 sheets defined 31.3% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A 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: 3.737A 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: 3.773A 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: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A 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: 3.559A 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: 3.538A 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: 3.648A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A 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: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A 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: 4.836A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A 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: 4.073A 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: 3.684A 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: 3.737A 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: 3.631A 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: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A 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: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A 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: 3.704A 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: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.622A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.736A 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: 3.718A 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: 3.560A 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: 4.070A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.801A 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: 3.529A 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: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.572A 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: 4.421A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.841A 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: 3.899A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.687A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.549A 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: 3.679A 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: 4.259A 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: 4.308A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.608A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.549A 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: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.662A 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: 3.752A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.526A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.928A 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: 3.850A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.579A 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: 3.647A 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: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.679A 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: 6.948A 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: 3.857A 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: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.050A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (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 327 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, 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=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A 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=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.603A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) 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: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A 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: 5.735A 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: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A 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: 3.582A 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: 4.730A 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: 4.713A 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: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.856A 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: 3.731A 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: 7.210A 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: 4.046A 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: 6.544A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.863A 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: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.601A 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=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.446A 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: 6.542A 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: 6.526A 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: 6.542A 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: 6.526A 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: 3.618A 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: 4.596A 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: 4.579A 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: 8.061A 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: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.293A 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: 3.876A 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: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A 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: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A 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 317 removed outlier: 4.220A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.569A 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: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A 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 Processing sheet with id=AE2, first strand: chain 'C' and resid 553 through 554 removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.452A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.837A 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=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A 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: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A 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: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A 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: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A 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: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, 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=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE9, 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=AE9 Processing sheet with id=AF1, 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) 1101 hydrogen bonds defined for protein. 3024 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: 6.07 Time building geometry restraints manager: 2.87 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: 6344 1.33 - 1.45: 7563 1.45 - 1.58: 15604 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 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.391 -0.061 1.18e-02 7.18e+03 2.70e+01 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.87e+01 bond pdb=" N PRO A 987 " pdb=" CD PRO A 987 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 29687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 39421 2.77 - 5.54: 882 5.54 - 8.31: 63 8.31 - 11.08: 5 11.08 - 13.85: 7 Bond angle restraints: 40378 Sorted by residual: angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.01 6.37 1.03e+00 9.43e-01 3.83e+01 angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.32 -9.56 1.59e+00 3.96e-01 3.61e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16182 17.94 - 35.88: 1738 35.88 - 53.82: 575 53.82 - 71.76: 189 71.76 - 89.70: 52 Dihedral angle restraints: 18736 sinusoidal: 8408 harmonic: 10328 Sorted by residual: 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 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 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 21.13 71.87 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 18733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4762 0.330 - 0.659: 6 0.659 - 0.989: 6 0.989 - 1.319: 2 1.319 - 1.648: 1 Chirality restraints: 4777 Sorted by residual: chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-02 2.50e+03 3.81e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " 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 Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.79e+01 ... (remaining 4774 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.354 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG b 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.16e+02 pdb=" C7 NAG b 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.126 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" CG ASN B 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.326 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.210 2.00e-02 2.50e+03 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 140 2.43 - 3.05: 17828 3.05 - 3.66: 40356 3.66 - 4.28: 64403 4.28 - 4.90: 106749 Nonbonded interactions: 229476 Sorted by model distance: nonbonded pdb=" O ASN A 536 " pdb=" CG LYS A 537 " model vdw 1.810 3.440 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 ... (remaining 229471 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' } 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: 1.570 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: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.590 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.012 0.528 29814 Z= 0.562 Angle : 1.331 71.321 40704 Z= 0.682 Chirality : 0.078 1.648 4777 Planarity : 0.009 0.306 5112 Dihedral : 17.596 89.703 11958 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 2.87 % Allowed : 9.10 % Favored : 88.03 % Rotamer: Outliers : 11.10 % Allowed : 15.90 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.11), residues: 3484 helix: -2.95 (0.12), residues: 991 sheet: -1.98 (0.17), residues: 743 loop : -3.31 (0.12), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP A 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01128 (29692) covalent geometry : angle 1.01332 (40378) SS BOND : bond 0.13410 ( 40) SS BOND : angle 13.89970 ( 80) hydrogen bonds : bond 0.22649 ( 1065) hydrogen bonds : angle 8.12035 ( 3024) link_BETA1-4 : bond 0.04362 ( 28) link_BETA1-4 : angle 6.51309 ( 84) link_NAG-ASN : bond 0.03448 ( 54) link_NAG-ASN : angle 8.47718 ( 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 832 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 345 poor density : 487 time to evaluate : 1.052 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.5334 (t80) cc_final: 0.4972 (t80) REVERT: A 369 TYR cc_start: 0.5212 (t80) cc_final: 0.4203 (t80) REVERT: A 599 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 692 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 856 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8209 (p0) REVERT: B 48 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 118 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7245 (tp) REVERT: B 153 MET cc_start: -0.0501 (mpp) cc_final: -0.2850 (ttp) REVERT: B 158 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.4812 (mpt180) REVERT: B 164 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.5291 (t0) REVERT: B 403 ARG cc_start: 0.5452 (OUTLIER) cc_final: 0.5125 (tpt170) REVERT: B 421 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5202 (p90) REVERT: B 535 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7152 (tttt) REVERT: B 710 ASN cc_start: 0.9518 (OUTLIER) cc_final: 0.9257 (p0) REVERT: B 748 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 856 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8446 (m110) REVERT: B 1030 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9110 (m) REVERT: C 153 MET cc_start: -0.3156 (mpp) cc_final: -0.3930 (ttm) REVERT: C 535 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6516 (ttmt) REVERT: D 82 MET cc_start: 0.5998 (mmt) cc_final: 0.3673 (tmm) REVERT: D 344 CYS cc_start: 0.4797 (OUTLIER) cc_final: 0.4481 (m) REVERT: D 379 ILE cc_start: 0.5351 (mm) cc_final: 0.4806 (tt) REVERT: D 462 MET cc_start: 0.6031 (mtp) cc_final: 0.5756 (ttt) REVERT: D 465 LYS cc_start: 0.2195 (ptpt) cc_final: 0.1943 (ttmt) REVERT: D 579 MET cc_start: 0.2163 (ptt) cc_final: 0.0835 (ttp) outliers start: 345 outliers final: 101 residues processed: 774 average time/residue: 0.1820 time to fit residues: 224.7301 Evaluate side-chains 349 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 232 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER 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 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE 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 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 281 GLU 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 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 344 CYS 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: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 207 HIS A 239 GLN A 271 GLN A 314 GLN A 422 ASN A 440 ASN A 498 GLN A 613 GLN A 644 GLN A 762 GLN A 764 ASN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1101 HIS B 81 ASN B 137 ASN B 188 ASN B 239 GLN B 314 GLN B 334 ASN B 360 ASN B 422 ASN B 440 ASN B 498 GLN B 564 GLN B 613 GLN B 644 GLN B 675 GLN B 710 ASN B 762 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 969 ASN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 207 HIS C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 498 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 703 ASN C 755 GLN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS D 42 GLN D 51 ASN D 58 ASN D 96 GLN D 134 ASN D 175 GLN D 239 HIS D 277 ASN D 330 ASN D 388 GLN D 401 HIS D 472 GLN D 505 HIS D 522 GLN D 586 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.169635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118570 restraints weight = 54340.648| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.49 r_work: 0.3154 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2789 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= 0.160 Angle : 0.793 13.383 40704 Z= 0.386 Chirality : 0.050 0.499 4777 Planarity : 0.005 0.061 5112 Dihedral : 10.707 97.138 5717 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.80 % Favored : 92.88 % Rotamer: Outliers : 5.47 % Allowed : 18.41 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.56 (0.13), residues: 3484 helix: -0.54 (0.16), residues: 975 sheet: -1.23 (0.18), residues: 737 loop : -2.64 (0.12), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 393 TYR 0.043 0.001 TYR B 396 PHE 0.032 0.002 PHE D 512 TRP 0.020 0.001 TRP D 477 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00350 (29692) covalent geometry : angle 0.75616 (40378) SS BOND : bond 0.00754 ( 40) SS BOND : angle 1.64047 ( 80) hydrogen bonds : bond 0.04876 ( 1065) hydrogen bonds : angle 5.56259 ( 3024) link_BETA1-4 : bond 0.00781 ( 28) link_BETA1-4 : angle 2.73126 ( 84) link_NAG-ASN : bond 0.00561 ( 54) link_NAG-ASN : angle 3.23052 ( 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 424 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 254 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6116 (t80) cc_final: 0.5877 (t80) REVERT: A 229 LEU cc_start: 0.8048 (tp) cc_final: 0.7708 (tp) REVERT: A 347 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: A 378 LYS cc_start: 0.6472 (mmtt) cc_final: 0.5937 (mttm) REVERT: A 508 TYR cc_start: 0.5881 (m-80) cc_final: 0.5592 (m-80) REVERT: A 690 GLN cc_start: 0.5836 (OUTLIER) cc_final: 0.5444 (mm-40) REVERT: A 703 ASN cc_start: 0.7530 (t0) cc_final: 0.7301 (t0) REVERT: A 794 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7756 (mm) REVERT: A 1005 GLN cc_start: 0.8751 (tp40) cc_final: 0.8531 (tp-100) REVERT: B 48 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 99 ASN cc_start: 0.8115 (m110) cc_final: 0.7738 (t0) REVERT: B 153 MET cc_start: -0.0661 (mpp) cc_final: -0.2913 (ttp) REVERT: B 158 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.4750 (mpt180) REVERT: B 217 PRO cc_start: 0.7936 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: B 377 PHE cc_start: 0.7793 (t80) cc_final: 0.7337 (t80) REVERT: B 514 SER cc_start: 0.7533 (t) cc_final: 0.7300 (m) REVERT: B 564 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: B 697 MET cc_start: 0.8949 (ptp) cc_final: 0.8704 (ptm) REVERT: B 990 GLU cc_start: 0.7509 (pp20) cc_final: 0.7100 (tt0) REVERT: B 991 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (m) REVERT: C 122 ASN cc_start: 0.2200 (OUTLIER) cc_final: 0.1624 (p0) REVERT: C 153 MET cc_start: -0.2874 (mpp) cc_final: -0.3433 (ttm) REVERT: C 298 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7894 (mm-30) REVERT: C 364 ASP cc_start: 0.7932 (m-30) cc_final: 0.6969 (t0) REVERT: C 529 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7379 (tppt) REVERT: C 855 PHE cc_start: 0.7006 (m-80) cc_final: 0.6607 (m-10) REVERT: D 62 MET cc_start: 0.3322 (tmm) cc_final: 0.2823 (ppp) REVERT: D 82 MET cc_start: 0.5969 (mmt) cc_final: 0.3796 (ptp) REVERT: D 270 MET cc_start: 0.3282 (ttm) cc_final: 0.3066 (ttm) REVERT: D 278 LEU cc_start: 0.3250 (mt) cc_final: 0.2951 (pp) REVERT: D 462 MET cc_start: 0.5542 (mtp) cc_final: 0.5147 (ttt) REVERT: D 465 LYS cc_start: 0.3295 (ptpt) cc_final: 0.2705 (tppt) REVERT: D 482 ARG cc_start: 0.2825 (mtt-85) cc_final: 0.2552 (mmm160) outliers start: 170 outliers final: 77 residues processed: 404 average time/residue: 0.1806 time to fit residues: 118.9354 Evaluate side-chains 273 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 187 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 301 CYS 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 500 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU 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 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 252 optimal weight: 0.4980 chunk 348 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 49 HIS B 314 GLN B 450 ASN B 613 GLN B 658 ASN B 675 GLN B 804 GLN B 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 675 GLN D 505 HIS D 599 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.165081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112899 restraints weight = 53753.694| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.39 r_work: 0.3065 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29814 Z= 0.230 Angle : 0.761 12.977 40704 Z= 0.368 Chirality : 0.050 0.506 4777 Planarity : 0.005 0.063 5112 Dihedral : 9.004 72.834 5586 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.93 % Rotamer: Outliers : 4.76 % Allowed : 18.44 % Favored : 76.79 % 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: -1.85 (0.13), residues: 3484 helix: 0.32 (0.17), residues: 988 sheet: -1.04 (0.19), residues: 697 loop : -2.27 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.021 0.002 TYR C1067 PHE 0.021 0.002 PHE B1103 TRP 0.026 0.002 TRP D 203 HIS 0.007 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00551 (29692) covalent geometry : angle 0.72649 (40378) SS BOND : bond 0.00429 ( 40) SS BOND : angle 1.69558 ( 80) hydrogen bonds : bond 0.05181 ( 1065) hydrogen bonds : angle 5.34037 ( 3024) link_BETA1-4 : bond 0.00597 ( 28) link_BETA1-4 : angle 2.52682 ( 84) link_NAG-ASN : bond 0.00398 ( 54) link_NAG-ASN : angle 3.05483 ( 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 367 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 219 time to evaluate : 1.067 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: A 378 LYS cc_start: 0.6669 (mmtt) cc_final: 0.6262 (mttp) REVERT: A 571 ASP cc_start: 0.8726 (m-30) cc_final: 0.8364 (t0) REVERT: A 916 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9293 (tp) REVERT: B 48 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8761 (mt) REVERT: B 153 MET cc_start: -0.0371 (mpp) cc_final: -0.2704 (ttp) REVERT: B 217 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: B 377 PHE cc_start: 0.7875 (t80) cc_final: 0.7517 (t80) REVERT: B 514 SER cc_start: 0.7593 (t) cc_final: 0.7210 (p) REVERT: B 699 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 153 MET cc_start: -0.2946 (mpp) cc_final: -0.3502 (ttm) REVERT: C 239 GLN cc_start: 0.7705 (tp40) cc_final: 0.7485 (tp40) REVERT: C 364 ASP cc_start: 0.7999 (m-30) cc_final: 0.7171 (t0) REVERT: C 535 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6022 (ttmt) REVERT: C 990 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 1132 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8684 (pp) REVERT: D 82 MET cc_start: 0.6176 (mmt) cc_final: 0.3916 (ptp) REVERT: D 133 CYS cc_start: 0.3535 (OUTLIER) cc_final: 0.3257 (t) REVERT: D 252 TYR cc_start: -0.0569 (m-10) cc_final: -0.0863 (m-10) REVERT: D 360 MET cc_start: 0.2192 (tpt) cc_final: 0.1833 (ttt) REVERT: D 579 MET cc_start: 0.1929 (ptt) cc_final: 0.0827 (ttp) outliers start: 148 outliers final: 92 residues processed: 356 average time/residue: 0.1607 time to fit residues: 96.7250 Evaluate side-chains 278 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 180 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 293 optimal weight: 0.9980 chunk 117 optimal weight: 0.0030 chunk 259 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 675 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN D 345 HIS D 442 GLN D 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113027 restraints weight = 53368.570| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.47 r_work: 0.3065 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29814 Z= 0.157 Angle : 0.697 12.001 40704 Z= 0.331 Chirality : 0.048 0.530 4777 Planarity : 0.004 0.063 5112 Dihedral : 8.381 72.471 5572 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 3.83 % Allowed : 20.02 % Favored : 76.15 % 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: -1.42 (0.14), residues: 3484 helix: 0.75 (0.17), residues: 990 sheet: -0.76 (0.19), residues: 712 loop : -2.07 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.021 0.001 TYR A 369 PHE 0.019 0.001 PHE A 347 TRP 0.028 0.001 TRP D 461 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00369 (29692) covalent geometry : angle 0.66496 (40378) SS BOND : bond 0.00386 ( 40) SS BOND : angle 1.50152 ( 80) hydrogen bonds : bond 0.04189 ( 1065) hydrogen bonds : angle 5.13118 ( 3024) link_BETA1-4 : bond 0.00641 ( 28) link_BETA1-4 : angle 2.46122 ( 84) link_NAG-ASN : bond 0.00338 ( 54) link_NAG-ASN : angle 2.78043 ( 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 314 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 195 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7645 (mt0) cc_final: 0.7344 (mt0) REVERT: A 347 PHE cc_start: 0.7716 (m-80) cc_final: 0.6609 (t80) REVERT: A 378 LYS cc_start: 0.6696 (mmtt) cc_final: 0.6128 (mttm) REVERT: A 393 THR cc_start: 0.7179 (m) cc_final: 0.6957 (m) REVERT: A 508 TYR cc_start: 0.5499 (m-80) cc_final: 0.5271 (m-80) REVERT: A 571 ASP cc_start: 0.8688 (m-30) cc_final: 0.8350 (t0) REVERT: A 856 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8500 (p0) REVERT: B 48 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8779 (mt) REVERT: B 377 PHE cc_start: 0.7917 (t80) cc_final: 0.7600 (t80) REVERT: B 529 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6668 (ptpp) REVERT: C 153 MET cc_start: -0.3102 (mpp) cc_final: -0.3583 (ttm) REVERT: C 191 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8415 (mt-10) REVERT: C 239 GLN cc_start: 0.7657 (tp40) cc_final: 0.7385 (tp40) REVERT: C 269 TYR cc_start: 0.7148 (m-10) cc_final: 0.6402 (m-80) REVERT: C 364 ASP cc_start: 0.8033 (m-30) cc_final: 0.7220 (t0) REVERT: C 519 HIS cc_start: 0.2553 (OUTLIER) cc_final: 0.2051 (m90) REVERT: C 535 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.5954 (ttmt) REVERT: C 1132 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8591 (pp) REVERT: D 82 MET cc_start: 0.6229 (mmt) cc_final: 0.4134 (ptp) REVERT: D 133 CYS cc_start: 0.3526 (OUTLIER) cc_final: 0.3173 (t) REVERT: D 278 LEU cc_start: 0.3264 (mt) cc_final: 0.2737 (tp) REVERT: D 482 ARG cc_start: 0.2653 (mtt-85) cc_final: 0.2361 (mmm160) REVERT: D 579 MET cc_start: 0.1927 (ptt) cc_final: 0.0901 (ttp) outliers start: 119 outliers final: 84 residues processed: 303 average time/residue: 0.1571 time to fit residues: 80.3983 Evaluate side-chains 267 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 176 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 189 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 150 optimal weight: 0.0270 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN A1011 GLN B 613 GLN B 675 GLN B 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 338 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111288 restraints weight = 53426.339| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 29814 Z= 0.220 Angle : 0.738 15.240 40704 Z= 0.348 Chirality : 0.050 0.512 4777 Planarity : 0.005 0.074 5112 Dihedral : 8.358 77.967 5567 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.41 % Favored : 92.39 % Rotamer: Outliers : 5.28 % Allowed : 18.76 % Favored : 75.96 % 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: -1.27 (0.14), residues: 3484 helix: 0.99 (0.17), residues: 985 sheet: -0.81 (0.19), residues: 719 loop : -1.99 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 995 TYR 0.022 0.002 TYR C1067 PHE 0.020 0.002 PHE C 157 TRP 0.016 0.001 TRP D 473 HIS 0.014 0.002 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00529 (29692) covalent geometry : angle 0.70386 (40378) SS BOND : bond 0.00438 ( 40) SS BOND : angle 1.57089 ( 80) hydrogen bonds : bond 0.04632 ( 1065) hydrogen bonds : angle 5.16241 ( 3024) link_BETA1-4 : bond 0.00790 ( 28) link_BETA1-4 : angle 2.67826 ( 84) link_NAG-ASN : bond 0.00946 ( 54) link_NAG-ASN : angle 2.88249 ( 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 360 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 196 time to evaluate : 1.056 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: A 129 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7600 (tptm) REVERT: A 239 GLN cc_start: 0.7874 (mt0) cc_final: 0.7575 (mm110) REVERT: A 343 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.5154 (t0) REVERT: A 347 PHE cc_start: 0.7771 (m-80) cc_final: 0.6742 (t80) REVERT: A 571 ASP cc_start: 0.8652 (m-30) cc_final: 0.8315 (t0) REVERT: A 787 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8772 (mm-40) REVERT: A 856 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8574 (p0) REVERT: B 377 PHE cc_start: 0.7927 (t80) cc_final: 0.7608 (t80) REVERT: B 529 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6888 (ptpp) REVERT: C 153 MET cc_start: -0.2837 (mpp) cc_final: -0.3140 (ttm) REVERT: C 269 TYR cc_start: 0.7295 (m-10) cc_final: 0.6593 (m-80) REVERT: C 364 ASP cc_start: 0.8054 (m-30) cc_final: 0.7192 (t0) REVERT: C 519 HIS cc_start: 0.2272 (OUTLIER) cc_final: 0.2027 (m90) REVERT: C 535 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.5911 (ttmt) REVERT: C 569 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6581 (mt) REVERT: C 1132 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8625 (pp) REVERT: D 82 MET cc_start: 0.6306 (mmt) cc_final: 0.4259 (ptp) REVERT: D 142 LEU cc_start: 0.3749 (mp) cc_final: 0.3111 (mm) REVERT: D 278 LEU cc_start: 0.3531 (mt) cc_final: 0.2934 (pp) REVERT: D 482 ARG cc_start: 0.2657 (mtt-85) cc_final: 0.2324 (mmm160) REVERT: D 579 MET cc_start: 0.2095 (ptt) cc_final: 0.1032 (ttp) outliers start: 164 outliers final: 104 residues processed: 347 average time/residue: 0.1748 time to fit residues: 102.1755 Evaluate side-chains 289 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 177 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 202 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN A 955 ASN B 675 GLN B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.162205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115134 restraints weight = 53374.292| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.52 r_work: 0.3054 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 29814 Z= 0.298 Angle : 0.792 13.464 40704 Z= 0.379 Chirality : 0.053 0.584 4777 Planarity : 0.005 0.071 5112 Dihedral : 8.476 83.282 5564 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 5.05 % Allowed : 19.25 % Favored : 75.70 % 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: -1.41 (0.14), residues: 3484 helix: 0.85 (0.17), residues: 990 sheet: -0.96 (0.18), residues: 717 loop : -2.02 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 995 TYR 0.024 0.002 TYR C1067 PHE 0.021 0.002 PHE B 140 TRP 0.016 0.002 TRP D 477 HIS 0.016 0.002 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00730 (29692) covalent geometry : angle 0.75709 (40378) SS BOND : bond 0.00572 ( 40) SS BOND : angle 1.95791 ( 80) hydrogen bonds : bond 0.05095 ( 1065) hydrogen bonds : angle 5.35489 ( 3024) link_BETA1-4 : bond 0.00563 ( 28) link_BETA1-4 : angle 2.59787 ( 84) link_NAG-ASN : bond 0.00410 ( 54) link_NAG-ASN : angle 3.03091 ( 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 349 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 192 time to evaluate : 1.069 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: A 239 GLN cc_start: 0.7922 (mt0) cc_final: 0.7669 (mm110) REVERT: A 378 LYS cc_start: 0.6555 (mmtt) cc_final: 0.5695 (mttp) REVERT: A 571 ASP cc_start: 0.8715 (m-30) cc_final: 0.8345 (t0) REVERT: A 856 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.8591 (p0) REVERT: A 950 ASP cc_start: 0.8701 (m-30) cc_final: 0.8480 (m-30) REVERT: B 111 ASP cc_start: 0.5050 (OUTLIER) cc_final: 0.4730 (m-30) REVERT: B 153 MET cc_start: 0.0094 (OUTLIER) cc_final: -0.2098 (ttp) REVERT: B 421 TYR cc_start: 0.5512 (OUTLIER) cc_final: 0.4061 (p90) REVERT: B 529 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7039 (ptpp) REVERT: C 535 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6082 (ttmt) REVERT: C 856 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8514 (p0) REVERT: C 1132 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8700 (pp) REVERT: D 82 MET cc_start: 0.6445 (mmt) cc_final: 0.4495 (ptp) REVERT: D 87 GLU cc_start: 0.5920 (mt-10) cc_final: 0.5696 (tt0) REVERT: D 142 LEU cc_start: 0.3858 (mp) cc_final: 0.3228 (mm) REVERT: D 462 MET cc_start: 0.4973 (ptm) cc_final: 0.4765 (tmm) REVERT: D 482 ARG cc_start: 0.2335 (mtt-85) cc_final: 0.1906 (mmm160) REVERT: D 579 MET cc_start: 0.2380 (ptt) cc_final: 0.1161 (ttp) outliers start: 157 outliers final: 113 residues processed: 332 average time/residue: 0.1688 time to fit residues: 94.4694 Evaluate side-chains 291 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 170 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 76 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 339 optimal weight: 6.9990 chunk 311 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 325 optimal weight: 0.3980 chunk 264 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 519 HIS B 675 GLN B 935 GLN C 422 ASN C 519 HIS D 34 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.165352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115086 restraints weight = 53526.336| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.42 r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29814 Z= 0.118 Angle : 0.669 12.397 40704 Z= 0.316 Chirality : 0.047 0.559 4777 Planarity : 0.004 0.064 5112 Dihedral : 7.707 78.930 5559 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.23 % Favored : 93.57 % Rotamer: Outliers : 3.51 % Allowed : 20.79 % Favored : 75.70 % 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: -0.99 (0.14), residues: 3484 helix: 1.22 (0.17), residues: 988 sheet: -0.61 (0.19), residues: 715 loop : -1.84 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.018 0.001 TYR A1067 PHE 0.021 0.001 PHE A 133 TRP 0.017 0.001 TRP D 477 HIS 0.012 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00267 (29692) covalent geometry : angle 0.63881 (40378) SS BOND : bond 0.00353 ( 40) SS BOND : angle 1.41444 ( 80) hydrogen bonds : bond 0.03599 ( 1065) hydrogen bonds : angle 4.98812 ( 3024) link_BETA1-4 : bond 0.00683 ( 28) link_BETA1-4 : angle 2.38602 ( 84) link_NAG-ASN : bond 0.00416 ( 54) link_NAG-ASN : angle 2.61350 ( 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 311 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 202 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7636 (tptm) REVERT: A 239 GLN cc_start: 0.7856 (mt0) cc_final: 0.7442 (mm110) REVERT: A 347 PHE cc_start: 0.7912 (m-80) cc_final: 0.6828 (t80) REVERT: A 571 ASP cc_start: 0.8597 (m-30) cc_final: 0.8205 (t0) REVERT: A 856 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8498 (p0) REVERT: B 153 MET cc_start: 0.0147 (mpp) cc_final: -0.2149 (ttp) REVERT: B 529 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7198 (ptpp) REVERT: C 191 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 194 PHE cc_start: 0.6129 (m-10) cc_final: 0.5920 (m-10) REVERT: C 239 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: C 269 TYR cc_start: 0.7292 (m-80) cc_final: 0.6717 (m-80) REVERT: C 535 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6057 (ttmt) REVERT: C 1132 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8554 (pp) REVERT: D 82 MET cc_start: 0.6332 (mmt) cc_final: 0.4471 (ptp) REVERT: D 142 LEU cc_start: 0.3367 (mp) cc_final: 0.2847 (mm) REVERT: D 278 LEU cc_start: 0.3324 (mt) cc_final: 0.2832 (pp) REVERT: D 357 ARG cc_start: 0.3895 (ptp-170) cc_final: 0.3490 (mtm110) REVERT: D 360 MET cc_start: 0.2448 (tpt) cc_final: 0.1924 (ttt) REVERT: D 462 MET cc_start: 0.5242 (ptm) cc_final: 0.4958 (ptm) REVERT: D 465 LYS cc_start: 0.2933 (mttp) cc_final: 0.1946 (ptmt) REVERT: D 482 ARG cc_start: 0.2368 (mtt-85) cc_final: 0.1988 (mmm160) REVERT: D 579 MET cc_start: 0.2238 (ptt) cc_final: 0.1056 (ttp) outliers start: 109 outliers final: 76 residues processed: 295 average time/residue: 0.1714 time to fit residues: 85.4027 Evaluate side-chains 267 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 186 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 188 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 68 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 348 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 191 optimal weight: 0.1980 chunk 222 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 341 optimal weight: 8.9990 overall best weight: 3.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 955 ASN B 519 HIS B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116144 restraints weight = 53372.016| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.44 r_work: 0.3074 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29814 Z= 0.219 Angle : 0.730 13.351 40704 Z= 0.345 Chirality : 0.050 0.542 4777 Planarity : 0.004 0.070 5112 Dihedral : 7.876 81.906 5558 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.46 % Favored : 92.39 % Rotamer: Outliers : 3.70 % Allowed : 20.70 % Favored : 75.60 % 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: -1.07 (0.14), residues: 3484 helix: 1.25 (0.17), residues: 983 sheet: -0.72 (0.19), residues: 708 loop : -1.90 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.022 0.001 TYR C1067 PHE 0.030 0.002 PHE C 429 TRP 0.020 0.001 TRP D 477 HIS 0.009 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00535 (29692) covalent geometry : angle 0.69971 (40378) SS BOND : bond 0.00578 ( 40) SS BOND : angle 1.57809 ( 80) hydrogen bonds : bond 0.04509 ( 1065) hydrogen bonds : angle 5.14207 ( 3024) link_BETA1-4 : bond 0.00537 ( 28) link_BETA1-4 : angle 2.44509 ( 84) link_NAG-ASN : bond 0.00363 ( 54) link_NAG-ASN : angle 2.71915 ( 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 308 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 0.871 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: A 40 ASP cc_start: 0.7672 (p0) cc_final: 0.7037 (t70) REVERT: A 129 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7593 (tptm) REVERT: A 347 PHE cc_start: 0.7951 (m-80) cc_final: 0.7115 (t80) REVERT: A 378 LYS cc_start: 0.6580 (mmtt) cc_final: 0.5582 (mttt) REVERT: A 571 ASP cc_start: 0.8654 (m-30) cc_final: 0.8262 (t0) REVERT: A 856 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8504 (p0) REVERT: B 153 MET cc_start: 0.0196 (OUTLIER) cc_final: -0.2123 (ttp) REVERT: B 529 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7289 (ptpp) REVERT: C 191 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: C 239 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: C 269 TYR cc_start: 0.7273 (m-80) cc_final: 0.6735 (m-80) REVERT: C 535 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6161 (ttmt) REVERT: C 1132 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8634 (pp) REVERT: D 82 MET cc_start: 0.6199 (mmt) cc_final: 0.4399 (ptp) REVERT: D 142 LEU cc_start: 0.3374 (mp) cc_final: 0.2858 (mm) REVERT: D 278 LEU cc_start: 0.3529 (mt) cc_final: 0.2952 (pp) REVERT: D 462 MET cc_start: 0.5130 (ptm) cc_final: 0.4821 (ptm) REVERT: D 465 LYS cc_start: 0.3005 (mttp) cc_final: 0.2076 (ptmt) REVERT: D 482 ARG cc_start: 0.2495 (mtt-85) cc_final: 0.2065 (mmm160) REVERT: D 579 MET cc_start: 0.2234 (ptt) cc_final: 0.1101 (ttp) outliers start: 115 outliers final: 99 residues processed: 293 average time/residue: 0.1686 time to fit residues: 83.8860 Evaluate side-chains 289 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 183 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 0.9990 chunk 313 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 233 optimal weight: 50.0000 chunk 238 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 755 GLN B 655 HIS B 675 GLN B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 101 GLN D 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.161762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115050 restraints weight = 53401.005| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.75 r_work: 0.3019 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 29814 Z= 0.278 Angle : 0.791 13.879 40704 Z= 0.377 Chirality : 0.052 0.561 4777 Planarity : 0.005 0.069 5112 Dihedral : 8.308 87.152 5558 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 3.89 % Allowed : 20.73 % Favored : 75.38 % 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: -1.27 (0.14), residues: 3484 helix: 1.07 (0.17), residues: 982 sheet: -0.78 (0.19), residues: 689 loop : -2.03 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.023 0.002 TYR C1067 PHE 0.037 0.002 PHE A 374 TRP 0.017 0.002 TRP D 349 HIS 0.009 0.002 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00680 (29692) covalent geometry : angle 0.75850 (40378) SS BOND : bond 0.00468 ( 40) SS BOND : angle 1.74025 ( 80) hydrogen bonds : bond 0.05011 ( 1065) hydrogen bonds : angle 5.31869 ( 3024) link_BETA1-4 : bond 0.00595 ( 28) link_BETA1-4 : angle 2.56888 ( 84) link_NAG-ASN : bond 0.00394 ( 54) link_NAG-ASN : angle 2.95098 ( 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 304 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 183 time to evaluate : 1.043 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: A 129 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7469 (tptm) REVERT: A 856 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8470 (p0) REVERT: A 950 ASP cc_start: 0.8779 (m-30) cc_final: 0.8570 (m-30) REVERT: B 153 MET cc_start: -0.0132 (OUTLIER) cc_final: -0.2276 (ttp) REVERT: B 529 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7619 (ptpp) REVERT: B 735 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 153 MET cc_start: 0.2722 (mmm) cc_final: 0.0034 (ptp) REVERT: C 191 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: C 269 TYR cc_start: 0.7308 (m-80) cc_final: 0.6846 (m-80) REVERT: C 535 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6158 (ttmt) REVERT: C 856 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8512 (p0) REVERT: C 1132 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8718 (pp) REVERT: D 82 MET cc_start: 0.6149 (mmt) cc_final: 0.4668 (ptp) REVERT: D 142 LEU cc_start: 0.3098 (mp) cc_final: 0.2770 (pp) REVERT: D 462 MET cc_start: 0.4706 (ptm) cc_final: 0.4412 (ptm) REVERT: D 465 LYS cc_start: 0.2927 (mttp) cc_final: 0.2065 (ptmt) REVERT: D 579 MET cc_start: 0.2258 (ptt) cc_final: 0.1200 (ttp) outliers start: 121 outliers final: 105 residues processed: 291 average time/residue: 0.1656 time to fit residues: 82.0825 Evaluate side-chains 283 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 170 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 115 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 312 optimal weight: 0.4980 chunk 223 optimal weight: 9.9990 chunk 305 optimal weight: 50.0000 chunk 317 optimal weight: 20.0000 chunk 320 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 762 GLN B 935 GLN C 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.161176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.113193 restraints weight = 53035.661| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.40 r_work: 0.3041 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 29814 Z= 0.307 Angle : 0.809 14.248 40704 Z= 0.385 Chirality : 0.053 0.555 4777 Planarity : 0.005 0.085 5112 Dihedral : 8.362 86.704 5558 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 4.09 % Allowed : 20.53 % Favored : 75.38 % 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: -1.41 (0.14), residues: 3484 helix: 0.95 (0.17), residues: 982 sheet: -0.92 (0.19), residues: 692 loop : -2.09 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.024 0.002 TYR C1067 PHE 0.036 0.002 PHE C 429 TRP 0.019 0.002 TRP D 477 HIS 0.052 0.002 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00751 (29692) covalent geometry : angle 0.77673 (40378) SS BOND : bond 0.00494 ( 40) SS BOND : angle 1.76741 ( 80) hydrogen bonds : bond 0.05109 ( 1065) hydrogen bonds : angle 5.37117 ( 3024) link_BETA1-4 : bond 0.00531 ( 28) link_BETA1-4 : angle 2.58915 ( 84) link_NAG-ASN : bond 0.00406 ( 54) link_NAG-ASN : angle 2.97966 ( 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 300 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 173 time to evaluate : 1.021 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 378 LYS cc_start: 0.6725 (mmtt) cc_final: 0.5637 (mtmm) REVERT: A 856 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (p0) REVERT: B 153 MET cc_start: -0.0137 (OUTLIER) cc_final: -0.2311 (ttp) REVERT: B 529 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7671 (ptpp) REVERT: B 735 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8263 (p) REVERT: C 153 MET cc_start: 0.2580 (mmm) cc_final: 0.0060 (ptp) REVERT: C 269 TYR cc_start: 0.7286 (m-80) cc_final: 0.6864 (m-80) REVERT: C 535 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6139 (ttmt) REVERT: C 1132 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8703 (pp) REVERT: D 82 MET cc_start: 0.6114 (mmt) cc_final: 0.4674 (ptp) REVERT: D 142 LEU cc_start: 0.3232 (mp) cc_final: 0.2739 (pp) REVERT: D 291 ILE cc_start: 0.1031 (pt) cc_final: 0.0827 (tp) REVERT: D 462 MET cc_start: 0.4593 (ptm) cc_final: 0.4304 (ptm) REVERT: D 465 LYS cc_start: 0.2771 (mttp) cc_final: 0.1939 (ptmt) REVERT: D 579 MET cc_start: 0.2047 (ptt) cc_final: 0.1112 (ttp) outliers start: 127 outliers final: 112 residues processed: 286 average time/residue: 0.1756 time to fit residues: 84.2022 Evaluate side-chains 279 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 161 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 69 optimal weight: 5.9990 chunk 348 optimal weight: 0.0050 chunk 337 optimal weight: 8.9990 chunk 270 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 532 ASN B 762 GLN B 935 GLN D 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.165059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117756 restraints weight = 53609.849| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.45 r_work: 0.3118 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29814 Z= 0.117 Angle : 0.682 12.844 40704 Z= 0.322 Chirality : 0.047 0.545 4777 Planarity : 0.004 0.075 5112 Dihedral : 7.585 85.805 5558 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.77 % Rotamer: Outliers : 3.12 % Allowed : 21.50 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -0.93 (0.14), residues: 3484 helix: 1.37 (0.17), residues: 979 sheet: -0.58 (0.19), residues: 699 loop : -1.84 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 567 TYR 0.019 0.001 TYR A1067 PHE 0.016 0.001 PHE A 133 TRP 0.021 0.001 TRP D 477 HIS 0.007 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00261 (29692) covalent geometry : angle 0.65481 (40378) SS BOND : bond 0.00381 ( 40) SS BOND : angle 1.30739 ( 80) hydrogen bonds : bond 0.03528 ( 1065) hydrogen bonds : angle 4.97049 ( 3024) link_BETA1-4 : bond 0.00709 ( 28) link_BETA1-4 : angle 2.30400 ( 84) link_NAG-ASN : bond 0.00394 ( 54) link_NAG-ASN : angle 2.53040 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10592.57 seconds wall clock time: 180 minutes 54.61 seconds (10854.61 seconds total)