Starting phenix.real_space_refine on Fri Mar 6 01:27:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.map" model { file = "/net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zge_11203/03_2026/6zge_11203.cif" } resolution = 2.6 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= 0.005 sd= 0.208 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 120 5.16 5 C 17121 2.51 5 N 4395 2.21 5 O 5355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26991 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "B" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "C" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 10.74, per 1000 atoms: 0.40 Number of scatterers: 26991 At special positions: 0 Unit cell: (151.093, 150.006, 179.355, 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 120 16.00 O 5355 8.00 N 4395 7.00 C 17121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1307 " - " ASN A 149 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 343 " " NAG A1317 " - " ASN A 657 " " NAG A1318 " - " ASN A 709 " " NAG A1323 " - " ASN A1074 " " NAG B1307 " - " ASN B 149 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 331 " " NAG B1314 " - " ASN B 343 " " NAG B1317 " - " ASN B 657 " " NAG B1318 " - " ASN B 709 " " NAG B1323 " - " ASN B1074 " " NAG C1307 " - " ASN C 149 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C 343 " " NAG C1317 " - " ASN C 657 " " NAG C1318 " - " ASN C 709 " " NAG C1323 " - " ASN C1074 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 61 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 61 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 2.1 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 24.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.138A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 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: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.335A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1056 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8310 1.34 - 1.47: 7203 1.47 - 1.59: 11889 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 27552 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 27547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 36229 2.34 - 4.69: 1169 4.69 - 7.03: 78 7.03 - 9.38: 12 9.38 - 11.72: 6 Bond angle restraints: 37494 Sorted by residual: angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.19 -8.39 2.13e+00 2.20e-01 1.55e+01 angle pdb=" CA LEU B 241 " pdb=" CB LEU B 241 " pdb=" CG LEU B 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 ... (remaining 37489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16240 17.58 - 35.16: 908 35.16 - 52.74: 189 52.74 - 70.32: 98 70.32 - 87.90: 28 Dihedral angle restraints: 17463 sinusoidal: 7857 harmonic: 9606 Sorted by residual: dihedral pdb=" CA HIS C 66 " pdb=" C HIS C 66 " pdb=" N ALA C 67 " pdb=" CA ALA C 67 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS A 66 " pdb=" C HIS A 66 " pdb=" N ALA A 67 " pdb=" CA ALA A 67 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 17460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2960 0.062 - 0.124: 1323 0.124 - 0.186: 158 0.186 - 0.248: 14 0.248 - 0.310: 3 Chirality restraints: 4458 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4455 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 539 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL B 539 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL B 539 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 540 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 539 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL C 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL C 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 9045 2.86 - 3.37: 21969 3.37 - 3.88: 43388 3.88 - 4.39: 50567 4.39 - 4.90: 87089 Nonbonded interactions: 212058 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 3.120 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.345 3.120 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.347 3.040 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 3.040 ... (remaining 212053 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1323)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.50 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 31.430 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.010 0.080 27678 Z= 0.406 Angle : 0.975 12.623 37827 Z= 0.516 Chirality : 0.063 0.310 4458 Planarity : 0.005 0.039 4755 Dihedral : 12.776 87.897 11160 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 0.73 % Allowed : 3.24 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3270 helix: 0.91 (0.19), residues: 711 sheet: 0.39 (0.18), residues: 777 loop : -1.87 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1039 TYR 0.024 0.003 TYR C 265 PHE 0.022 0.004 PHE A 592 TRP 0.017 0.003 TRP B 886 HIS 0.008 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00983 (27552) covalent geometry : angle 0.94125 (37494) SS BOND : bond 0.01125 ( 45) SS BOND : angle 2.26032 ( 90) hydrogen bonds : bond 0.14378 ( 1056) hydrogen bonds : angle 6.58130 ( 2856) link_BETA1-4 : bond 0.00483 ( 30) link_BETA1-4 : angle 1.54371 ( 90) link_NAG-ASN : bond 0.00540 ( 51) link_NAG-ASN : angle 3.70711 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 408 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8415 (m-40) cc_final: 0.8139 (m110) REVERT: A 158 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7992 (mtt90) REVERT: A 505 TYR cc_start: 0.7701 (m-80) cc_final: 0.7267 (t80) REVERT: A 765 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7713 (mtp180) REVERT: A 904 TYR cc_start: 0.7986 (m-10) cc_final: 0.7220 (m-10) REVERT: A 947 LYS cc_start: 0.8420 (mttm) cc_final: 0.8208 (mppt) REVERT: A 957 GLN cc_start: 0.8066 (tt0) cc_final: 0.7760 (tp40) REVERT: B 88 ASP cc_start: 0.7743 (m-30) cc_final: 0.7510 (m-30) REVERT: B 259 THR cc_start: 0.8180 (t) cc_final: 0.7974 (m) REVERT: B 321 GLN cc_start: 0.8447 (mm110) cc_final: 0.8176 (mm110) REVERT: B 430 THR cc_start: 0.8451 (m) cc_final: 0.8228 (m) REVERT: B 505 TYR cc_start: 0.7829 (m-80) cc_final: 0.7442 (t80) REVERT: B 646 ARG cc_start: 0.8255 (mtm180) cc_final: 0.8028 (mtp180) REVERT: B 705 VAL cc_start: 0.8419 (t) cc_final: 0.8190 (t) REVERT: B 738 CYS cc_start: 0.6106 (t) cc_final: 0.5567 (t) REVERT: B 916 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 947 LYS cc_start: 0.8456 (mttm) cc_final: 0.8087 (mppt) REVERT: B 955 ASN cc_start: 0.7895 (m-40) cc_final: 0.7549 (m110) REVERT: B 1005 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8106 (tp-100) REVERT: B 1107 ARG cc_start: 0.7740 (mpp80) cc_final: 0.6820 (mtt180) REVERT: B 1125 ASN cc_start: 0.7878 (p0) cc_final: 0.7545 (p0) REVERT: B 1141 LEU cc_start: 0.8269 (tp) cc_final: 0.8009 (tm) REVERT: C 88 ASP cc_start: 0.7651 (m-30) cc_final: 0.7437 (m-30) REVERT: C 505 TYR cc_start: 0.7755 (m-80) cc_final: 0.7257 (t80) REVERT: C 759 PHE cc_start: 0.7238 (m-80) cc_final: 0.6975 (m-80) REVERT: C 869 MET cc_start: 0.8716 (mtt) cc_final: 0.8461 (mtp) REVERT: C 904 TYR cc_start: 0.7968 (m-10) cc_final: 0.6945 (m-10) REVERT: C 947 LYS cc_start: 0.8261 (mttm) cc_final: 0.7907 (mppt) REVERT: C 1073 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7421 (tttp) outliers start: 21 outliers final: 3 residues processed: 426 average time/residue: 0.6837 time to fit residues: 335.0320 Evaluate side-chains 261 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 257 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0060 chunk 298 optimal weight: 0.9980 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 218 GLN A 239 GLN A 245 HIS A 394 ASN A 440 ASN A 474 GLN A 501 ASN A 540 ASN A 563 GLN A 580 GLN A 641 ASN A 658 ASN A 751 ASN A 925 ASN A 954 GLN A 969 ASN A1023 ASN A1036 GLN A1064 HIS B 99 ASN B 146 HIS B 239 GLN B 245 HIS B 394 ASN B 474 GLN B 501 ASN B 540 ASN B 580 GLN B 641 ASN B 658 ASN B 675 GLN B 751 ASN B 925 ASN B 935 GLN B1023 ASN B1036 GLN B1064 HIS C 99 ASN C 188 ASN C 207 HIS C 218 GLN C 239 GLN C 245 HIS C 314 GLN C 394 ASN C 474 GLN C 501 ASN C 540 ASN C 580 GLN C 613 GLN C 641 ASN C 658 ASN C 703 ASN C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116311 restraints weight = 36635.816| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.15 r_work: 0.3080 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 27678 Z= 0.147 Angle : 0.701 16.523 37827 Z= 0.355 Chirality : 0.049 0.438 4458 Planarity : 0.004 0.044 4755 Dihedral : 7.807 59.616 5264 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.29 % Allowed : 8.00 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3270 helix: 1.26 (0.20), residues: 714 sheet: 0.49 (0.19), residues: 765 loop : -1.77 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 246 TYR 0.017 0.001 TYR B 265 PHE 0.014 0.001 PHE B 643 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00311 (27552) covalent geometry : angle 0.65152 (37494) SS BOND : bond 0.01221 ( 45) SS BOND : angle 2.67710 ( 90) hydrogen bonds : bond 0.06031 ( 1056) hydrogen bonds : angle 5.56365 ( 2856) link_BETA1-4 : bond 0.00391 ( 30) link_BETA1-4 : angle 1.37349 ( 90) link_NAG-ASN : bond 0.00974 ( 51) link_NAG-ASN : angle 3.49461 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.7931 (mtt180) REVERT: A 271 GLN cc_start: 0.8569 (mt0) cc_final: 0.8323 (mt0) REVERT: A 312 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8976 (tt) REVERT: A 394 ASN cc_start: 0.8625 (m-40) cc_final: 0.8139 (m110) REVERT: A 505 TYR cc_start: 0.8479 (m-80) cc_final: 0.7566 (t80) REVERT: A 738 CYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7671 (t) REVERT: A 745 ASP cc_start: 0.7744 (m-30) cc_final: 0.7332 (m-30) REVERT: A 869 MET cc_start: 0.8943 (mtt) cc_final: 0.8651 (mtm) REVERT: A 904 TYR cc_start: 0.8473 (m-10) cc_final: 0.7420 (m-10) REVERT: A 947 LYS cc_start: 0.8678 (mttm) cc_final: 0.8115 (mppt) REVERT: A 955 ASN cc_start: 0.7787 (m-40) cc_final: 0.7569 (m110) REVERT: A 957 GLN cc_start: 0.8699 (tt0) cc_final: 0.8371 (tp40) REVERT: B 80 ASP cc_start: 0.7940 (m-30) cc_final: 0.7722 (m-30) REVERT: B 153 MET cc_start: 0.7803 (ptm) cc_final: 0.7520 (ptt) REVERT: B 312 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8912 (tp) REVERT: B 321 GLN cc_start: 0.8594 (mm110) cc_final: 0.8241 (mm110) REVERT: B 505 TYR cc_start: 0.8495 (m-80) cc_final: 0.7574 (t80) REVERT: B 646 ARG cc_start: 0.8326 (mtm180) cc_final: 0.8005 (mtp180) REVERT: B 661 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: B 705 VAL cc_start: 0.8294 (t) cc_final: 0.8021 (t) REVERT: B 738 CYS cc_start: 0.8146 (t) cc_final: 0.7813 (t) REVERT: B 745 ASP cc_start: 0.7505 (m-30) cc_final: 0.7239 (m-30) REVERT: B 916 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 947 LYS cc_start: 0.8555 (mttm) cc_final: 0.7913 (mppt) REVERT: B 955 ASN cc_start: 0.7838 (m-40) cc_final: 0.7505 (m-40) REVERT: B 1073 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7818 (tttm) REVERT: B 1091 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8200 (mtt-85) REVERT: B 1107 ARG cc_start: 0.8088 (mpp80) cc_final: 0.7241 (mtt180) REVERT: B 1125 ASN cc_start: 0.8058 (p0) cc_final: 0.7631 (p0) REVERT: C 187 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7275 (mmtm) REVERT: C 202 LYS cc_start: 0.9135 (mttt) cc_final: 0.8887 (mtpm) REVERT: C 246 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7220 (mtt90) REVERT: C 394 ASN cc_start: 0.8633 (m-40) cc_final: 0.8227 (m110) REVERT: C 505 TYR cc_start: 0.8512 (m-80) cc_final: 0.7568 (t80) REVERT: C 738 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7695 (t) REVERT: C 745 ASP cc_start: 0.7663 (m-30) cc_final: 0.7449 (m-30) REVERT: C 904 TYR cc_start: 0.8516 (m-10) cc_final: 0.7354 (m-10) REVERT: C 947 LYS cc_start: 0.8582 (mttm) cc_final: 0.7988 (mppt) REVERT: C 1010 GLN cc_start: 0.8968 (mt0) cc_final: 0.8765 (mm-40) REVERT: C 1073 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7573 (tttp) outliers start: 37 outliers final: 14 residues processed: 343 average time/residue: 0.6402 time to fit residues: 254.2447 Evaluate side-chains 303 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 248 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 0.0030 chunk 188 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 563 GLN A 613 GLN A 954 GLN B 99 ASN B 658 ASN B 762 GLN B 969 ASN C 99 ASN C 207 HIS C 658 ASN C 762 GLN C 787 GLN C1005 GLN C1054 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111790 restraints weight = 50549.958| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.48 r_work: 0.2973 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 27678 Z= 0.184 Angle : 0.730 15.126 37827 Z= 0.375 Chirality : 0.051 0.474 4458 Planarity : 0.005 0.049 4755 Dihedral : 7.307 58.700 5264 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.74 % Rotamer: Outliers : 2.16 % Allowed : 8.70 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3270 helix: 1.15 (0.20), residues: 714 sheet: 0.59 (0.18), residues: 756 loop : -1.81 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.024 0.002 TYR B 265 PHE 0.018 0.002 PHE A 802 TRP 0.016 0.002 TRP A 152 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00433 (27552) covalent geometry : angle 0.68970 (37494) SS BOND : bond 0.00830 ( 45) SS BOND : angle 2.99464 ( 90) hydrogen bonds : bond 0.06907 ( 1056) hydrogen bonds : angle 5.53519 ( 2856) link_BETA1-4 : bond 0.00375 ( 30) link_BETA1-4 : angle 1.21077 ( 90) link_NAG-ASN : bond 0.00647 ( 51) link_NAG-ASN : angle 3.01205 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8958 (tt) REVERT: A 394 ASN cc_start: 0.8592 (m-40) cc_final: 0.8144 (m110) REVERT: A 505 TYR cc_start: 0.8399 (m-80) cc_final: 0.7853 (t80) REVERT: A 904 TYR cc_start: 0.8453 (m-10) cc_final: 0.7325 (m-10) REVERT: A 947 LYS cc_start: 0.8689 (mttm) cc_final: 0.8306 (mppt) REVERT: A 955 ASN cc_start: 0.7949 (m-40) cc_final: 0.7665 (m110) REVERT: A 957 GLN cc_start: 0.8666 (tt0) cc_final: 0.8377 (tp40) REVERT: B 154 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: B 321 GLN cc_start: 0.8644 (mm110) cc_final: 0.8325 (mm110) REVERT: B 505 TYR cc_start: 0.8383 (m-80) cc_final: 0.7742 (t80) REVERT: B 646 ARG cc_start: 0.8433 (mtm180) cc_final: 0.8104 (mtp180) REVERT: B 661 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: B 738 CYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7630 (t) REVERT: B 947 LYS cc_start: 0.8524 (mttm) cc_final: 0.8009 (mppt) REVERT: B 955 ASN cc_start: 0.7828 (m-40) cc_final: 0.7552 (m-40) REVERT: B 1073 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7855 (tttm) REVERT: B 1125 ASN cc_start: 0.8083 (p0) cc_final: 0.7689 (p0) REVERT: C 187 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7625 (mmtm) REVERT: C 246 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7424 (mtt90) REVERT: C 505 TYR cc_start: 0.8492 (m-80) cc_final: 0.7844 (t80) REVERT: C 738 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7488 (t) REVERT: C 745 ASP cc_start: 0.7544 (m-30) cc_final: 0.7274 (m-30) REVERT: C 947 LYS cc_start: 0.8335 (mttm) cc_final: 0.7909 (mppt) REVERT: C 1045 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8126 (tttp) REVERT: C 1073 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7645 (tttp) outliers start: 62 outliers final: 30 residues processed: 320 average time/residue: 0.6308 time to fit residues: 234.7580 Evaluate side-chains 300 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 326 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 298 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 474 GLN A 563 GLN A 613 GLN A 913 GLN A 954 GLN B 99 ASN B 218 GLN B 440 ASN B 474 GLN B 658 ASN B 762 GLN B 779 GLN C 99 ASN C 207 HIS C 474 GLN C 658 ASN C 901 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112536 restraints weight = 45748.290| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.54 r_work: 0.3012 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27678 Z= 0.170 Angle : 0.709 11.840 37827 Z= 0.364 Chirality : 0.050 0.435 4458 Planarity : 0.005 0.055 4755 Dihedral : 6.937 59.631 5260 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 9.08 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3270 helix: 1.14 (0.20), residues: 714 sheet: 0.64 (0.18), residues: 765 loop : -1.84 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1000 TYR 0.022 0.002 TYR B 265 PHE 0.024 0.002 PHE C 133 TRP 0.012 0.002 TRP A 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (27552) covalent geometry : angle 0.66617 (37494) SS BOND : bond 0.00610 ( 45) SS BOND : angle 3.28049 ( 90) hydrogen bonds : bond 0.06578 ( 1056) hydrogen bonds : angle 5.46154 ( 2856) link_BETA1-4 : bond 0.00353 ( 30) link_BETA1-4 : angle 1.22126 ( 90) link_NAG-ASN : bond 0.00523 ( 51) link_NAG-ASN : angle 2.86251 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 0.974 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 113 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8235 (mttt) REVERT: A 158 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8361 (mtt180) REVERT: A 394 ASN cc_start: 0.8736 (m-40) cc_final: 0.8243 (m110) REVERT: A 505 TYR cc_start: 0.8559 (m-80) cc_final: 0.7733 (t80) REVERT: A 613 GLN cc_start: 0.8598 (mt0) cc_final: 0.8303 (mt0) REVERT: A 705 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7868 (t) REVERT: A 869 MET cc_start: 0.9021 (mtt) cc_final: 0.8766 (mtm) REVERT: A 904 TYR cc_start: 0.8548 (m-10) cc_final: 0.7445 (m-10) REVERT: A 947 LYS cc_start: 0.8807 (mttm) cc_final: 0.8210 (mppt) REVERT: A 955 ASN cc_start: 0.7983 (m-40) cc_final: 0.7565 (m110) REVERT: A 957 GLN cc_start: 0.8710 (tt0) cc_final: 0.8391 (tp40) REVERT: B 154 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 321 GLN cc_start: 0.8576 (mm110) cc_final: 0.8221 (mm110) REVERT: B 394 ASN cc_start: 0.8914 (m-40) cc_final: 0.8538 (m110) REVERT: B 505 TYR cc_start: 0.8580 (m-80) cc_final: 0.7608 (t80) REVERT: B 646 ARG cc_start: 0.8417 (mtm180) cc_final: 0.8046 (mtp180) REVERT: B 661 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: B 738 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7925 (t) REVERT: B 947 LYS cc_start: 0.8614 (mttm) cc_final: 0.7895 (mppt) REVERT: B 955 ASN cc_start: 0.7835 (m-40) cc_final: 0.7598 (m-40) REVERT: B 1073 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7855 (tttm) REVERT: B 1125 ASN cc_start: 0.8026 (p0) cc_final: 0.7561 (p0) REVERT: C 66 HIS cc_start: 0.7915 (m-70) cc_final: 0.7509 (m-70) REVERT: C 246 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6964 (mtt90) REVERT: C 394 ASN cc_start: 0.8808 (m-40) cc_final: 0.8390 (m110) REVERT: C 505 TYR cc_start: 0.8666 (m-80) cc_final: 0.7708 (t80) REVERT: C 738 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7738 (t) REVERT: C 745 ASP cc_start: 0.7655 (m-30) cc_final: 0.7391 (m-30) REVERT: C 947 LYS cc_start: 0.8506 (mttm) cc_final: 0.7869 (mppt) REVERT: C 1045 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8231 (tttp) REVERT: C 1073 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7688 (ttpp) outliers start: 65 outliers final: 35 residues processed: 307 average time/residue: 0.6240 time to fit residues: 223.2917 Evaluate side-chains 303 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 222 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 128 optimal weight: 0.0470 chunk 322 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 563 GLN A 954 GLN B 30 ASN B 99 ASN B 218 GLN B 658 ASN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114135 restraints weight = 52707.557| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.29 r_work: 0.2991 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27678 Z= 0.140 Angle : 0.658 16.716 37827 Z= 0.336 Chirality : 0.048 0.449 4458 Planarity : 0.004 0.050 4755 Dihedral : 6.640 59.851 5258 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.77 % Allowed : 10.19 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3270 helix: 1.30 (0.20), residues: 714 sheet: 0.75 (0.18), residues: 783 loop : -1.83 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B 265 PHE 0.015 0.001 PHE C 133 TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00318 (27552) covalent geometry : angle 0.62038 (37494) SS BOND : bond 0.00595 ( 45) SS BOND : angle 2.80762 ( 90) hydrogen bonds : bond 0.05887 ( 1056) hydrogen bonds : angle 5.33600 ( 2856) link_BETA1-4 : bond 0.00382 ( 30) link_BETA1-4 : angle 1.15580 ( 90) link_NAG-ASN : bond 0.00423 ( 51) link_NAG-ASN : angle 2.67433 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8293 (mttt) REVERT: A 158 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8318 (mtt180) REVERT: A 394 ASN cc_start: 0.8624 (m-40) cc_final: 0.8208 (m110) REVERT: A 505 TYR cc_start: 0.8332 (m-80) cc_final: 0.7894 (t80) REVERT: A 613 GLN cc_start: 0.8499 (mt0) cc_final: 0.8250 (mt0) REVERT: A 738 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7559 (t) REVERT: A 762 GLN cc_start: 0.8489 (tt0) cc_final: 0.8133 (mt0) REVERT: A 869 MET cc_start: 0.8960 (mtt) cc_final: 0.8692 (mtm) REVERT: A 904 TYR cc_start: 0.8419 (m-10) cc_final: 0.7401 (m-10) REVERT: A 947 LYS cc_start: 0.8685 (mttm) cc_final: 0.8252 (mppt) REVERT: A 955 ASN cc_start: 0.7905 (m-40) cc_final: 0.7489 (m110) REVERT: A 957 GLN cc_start: 0.8692 (tt0) cc_final: 0.8406 (tp40) REVERT: B 321 GLN cc_start: 0.8599 (mm110) cc_final: 0.8295 (mm110) REVERT: B 394 ASN cc_start: 0.8681 (m-40) cc_final: 0.8448 (m110) REVERT: B 505 TYR cc_start: 0.8419 (m-80) cc_final: 0.7807 (t80) REVERT: B 646 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8088 (mtp180) REVERT: B 661 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: B 738 CYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7667 (t) REVERT: B 947 LYS cc_start: 0.8520 (mttm) cc_final: 0.7971 (mppt) REVERT: B 955 ASN cc_start: 0.7742 (m-40) cc_final: 0.7512 (m-40) REVERT: B 1073 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7897 (tttm) REVERT: B 1113 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: B 1125 ASN cc_start: 0.7993 (p0) cc_final: 0.7588 (p0) REVERT: C 246 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7137 (mtt90) REVERT: C 323 THR cc_start: 0.8448 (p) cc_final: 0.8180 (p) REVERT: C 394 ASN cc_start: 0.8684 (m-40) cc_final: 0.8300 (m110) REVERT: C 505 TYR cc_start: 0.8479 (m-80) cc_final: 0.7850 (t80) REVERT: C 738 CYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7583 (t) REVERT: C 745 ASP cc_start: 0.7631 (m-30) cc_final: 0.7263 (m-30) REVERT: C 844 ILE cc_start: 0.6814 (mp) cc_final: 0.6567 (mt) REVERT: C 947 LYS cc_start: 0.8368 (mttm) cc_final: 0.7874 (mppt) REVERT: C 1045 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8119 (tttp) REVERT: C 1073 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7544 (tttp) outliers start: 51 outliers final: 28 residues processed: 302 average time/residue: 0.6151 time to fit residues: 217.3933 Evaluate side-chains 291 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 176 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 290 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 954 GLN B 99 ASN B 164 ASN B 218 GLN B 474 GLN B 658 ASN B 762 GLN B 787 GLN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111604 restraints weight = 51580.977| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.42 r_work: 0.2967 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 27678 Z= 0.190 Angle : 0.730 19.908 37827 Z= 0.375 Chirality : 0.051 0.461 4458 Planarity : 0.005 0.052 4755 Dihedral : 6.729 59.846 5258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 2.40 % Allowed : 10.40 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3270 helix: 1.11 (0.20), residues: 711 sheet: 0.70 (0.18), residues: 786 loop : -1.86 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1000 TYR 0.024 0.002 TYR B 265 PHE 0.018 0.002 PHE B 133 TRP 0.011 0.002 TRP A 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00455 (27552) covalent geometry : angle 0.69090 (37494) SS BOND : bond 0.00773 ( 45) SS BOND : angle 3.27373 ( 90) hydrogen bonds : bond 0.06924 ( 1056) hydrogen bonds : angle 5.45752 ( 2856) link_BETA1-4 : bond 0.00364 ( 30) link_BETA1-4 : angle 1.13084 ( 90) link_NAG-ASN : bond 0.00453 ( 51) link_NAG-ASN : angle 2.77587 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: A 158 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8348 (mtt180) REVERT: A 394 ASN cc_start: 0.8628 (m-40) cc_final: 0.8163 (m110) REVERT: A 505 TYR cc_start: 0.8363 (m-80) cc_final: 0.7889 (t80) REVERT: A 613 GLN cc_start: 0.8604 (mt0) cc_final: 0.8362 (mt0) REVERT: A 705 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 869 MET cc_start: 0.9009 (mtt) cc_final: 0.8782 (mtm) REVERT: A 904 TYR cc_start: 0.8446 (m-10) cc_final: 0.7412 (m-10) REVERT: A 947 LYS cc_start: 0.8711 (mttm) cc_final: 0.8239 (mppt) REVERT: A 955 ASN cc_start: 0.7937 (m-40) cc_final: 0.7495 (m110) REVERT: A 957 GLN cc_start: 0.8691 (tt0) cc_final: 0.8413 (tp40) REVERT: A 1005 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8581 (tp-100) REVERT: B 154 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 215 ASP cc_start: 0.7298 (m-30) cc_final: 0.6918 (m-30) REVERT: B 321 GLN cc_start: 0.8585 (mm110) cc_final: 0.8295 (mm110) REVERT: B 394 ASN cc_start: 0.8725 (m-40) cc_final: 0.8462 (m-40) REVERT: B 505 TYR cc_start: 0.8431 (m-80) cc_final: 0.7823 (t80) REVERT: B 646 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7985 (mtp180) REVERT: B 661 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: B 738 CYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7647 (t) REVERT: B 947 LYS cc_start: 0.8606 (mttm) cc_final: 0.8032 (mppt) REVERT: B 955 ASN cc_start: 0.7807 (m-40) cc_final: 0.7550 (m-40) REVERT: B 1073 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: B 1125 ASN cc_start: 0.8034 (p0) cc_final: 0.7638 (p0) REVERT: C 246 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7165 (mtt90) REVERT: C 323 THR cc_start: 0.8442 (p) cc_final: 0.8179 (p) REVERT: C 357 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8080 (tpp-160) REVERT: C 394 ASN cc_start: 0.8708 (m-40) cc_final: 0.8407 (m110) REVERT: C 505 TYR cc_start: 0.8494 (m-80) cc_final: 0.7843 (t80) REVERT: C 738 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7466 (t) REVERT: C 947 LYS cc_start: 0.8410 (mttm) cc_final: 0.7950 (mppt) REVERT: C 1045 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8144 (tttp) REVERT: C 1073 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7612 (ttpp) outliers start: 69 outliers final: 42 residues processed: 304 average time/residue: 0.5975 time to fit residues: 213.0371 Evaluate side-chains 304 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 195 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 259 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 262 optimal weight: 0.2980 chunk 287 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 314 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 474 GLN A 563 GLN A 787 GLN A 954 GLN B 66 HIS B 99 ASN B 218 GLN B 658 ASN C 66 HIS C 99 ASN C 164 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115486 restraints weight = 49168.938| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.28 r_work: 0.3029 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27678 Z= 0.123 Angle : 0.635 15.373 37827 Z= 0.323 Chirality : 0.047 0.386 4458 Planarity : 0.004 0.051 4755 Dihedral : 6.484 58.167 5258 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.60 % Allowed : 11.48 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % 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: -0.58 (0.14), residues: 3270 helix: 1.41 (0.20), residues: 711 sheet: 0.78 (0.18), residues: 789 loop : -1.80 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.017 0.001 TYR B 265 PHE 0.016 0.001 PHE C 133 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00270 (27552) covalent geometry : angle 0.59866 (37494) SS BOND : bond 0.00532 ( 45) SS BOND : angle 2.76328 ( 90) hydrogen bonds : bond 0.05325 ( 1056) hydrogen bonds : angle 5.25373 ( 2856) link_BETA1-4 : bond 0.00375 ( 30) link_BETA1-4 : angle 1.14408 ( 90) link_NAG-ASN : bond 0.00416 ( 51) link_NAG-ASN : angle 2.55273 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8305 (mttt) REVERT: A 158 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8237 (mtt180) REVERT: A 215 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: A 394 ASN cc_start: 0.8592 (m-40) cc_final: 0.8190 (m110) REVERT: A 505 TYR cc_start: 0.8310 (m-80) cc_final: 0.7858 (t80) REVERT: A 613 GLN cc_start: 0.8364 (mt0) cc_final: 0.8137 (mt0) REVERT: A 738 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7500 (t) REVERT: A 762 GLN cc_start: 0.8304 (tt0) cc_final: 0.8037 (mt0) REVERT: A 869 MET cc_start: 0.8916 (mtt) cc_final: 0.8626 (mtm) REVERT: A 904 TYR cc_start: 0.8397 (m-10) cc_final: 0.7402 (m-10) REVERT: A 947 LYS cc_start: 0.8633 (mttm) cc_final: 0.8219 (mppt) REVERT: A 955 ASN cc_start: 0.7850 (m-40) cc_final: 0.7450 (m110) REVERT: A 957 GLN cc_start: 0.8682 (tt0) cc_final: 0.8395 (tp40) REVERT: B 215 ASP cc_start: 0.7266 (m-30) cc_final: 0.6861 (m-30) REVERT: B 321 GLN cc_start: 0.8566 (mm110) cc_final: 0.8294 (mm110) REVERT: B 394 ASN cc_start: 0.8705 (m-40) cc_final: 0.8447 (m110) REVERT: B 505 TYR cc_start: 0.8353 (m-80) cc_final: 0.7805 (t80) REVERT: B 646 ARG cc_start: 0.8441 (mtm180) cc_final: 0.8069 (mtp180) REVERT: B 661 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: B 738 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (t) REVERT: B 882 ILE cc_start: 0.8666 (pt) cc_final: 0.8443 (mt) REVERT: B 947 LYS cc_start: 0.8482 (mttm) cc_final: 0.7964 (mppt) REVERT: B 955 ASN cc_start: 0.7689 (m-40) cc_final: 0.7450 (m-40) REVERT: B 1073 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (tttm) REVERT: B 1125 ASN cc_start: 0.7970 (p0) cc_final: 0.7525 (p0) REVERT: C 66 HIS cc_start: 0.7755 (m90) cc_final: 0.7387 (m-70) REVERT: C 187 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7611 (mppt) REVERT: C 246 ARG cc_start: 0.7580 (mtt90) cc_final: 0.7211 (mtt90) REVERT: C 323 THR cc_start: 0.8386 (p) cc_final: 0.8122 (p) REVERT: C 394 ASN cc_start: 0.8650 (m-40) cc_final: 0.8266 (m110) REVERT: C 505 TYR cc_start: 0.8414 (m-80) cc_final: 0.7828 (t80) REVERT: C 738 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7518 (t) REVERT: C 904 TYR cc_start: 0.8452 (m-10) cc_final: 0.7465 (m-10) REVERT: C 947 LYS cc_start: 0.8350 (mttm) cc_final: 0.7920 (mppt) REVERT: C 1045 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8066 (tttp) REVERT: C 1073 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7495 (tttp) outliers start: 46 outliers final: 20 residues processed: 288 average time/residue: 0.6491 time to fit residues: 217.9273 Evaluate side-chains 288 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 191 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.0000 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114374 restraints weight = 42294.308| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.52 r_work: 0.3042 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27678 Z= 0.136 Angle : 0.650 13.577 37827 Z= 0.332 Chirality : 0.048 0.401 4458 Planarity : 0.004 0.049 4755 Dihedral : 6.448 57.461 5258 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 1.46 % Allowed : 11.80 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3270 helix: 1.41 (0.20), residues: 711 sheet: 0.76 (0.18), residues: 777 loop : -1.79 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.020 0.001 TYR B 265 PHE 0.015 0.001 PHE A 643 TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (27552) covalent geometry : angle 0.61407 (37494) SS BOND : bond 0.00544 ( 45) SS BOND : angle 2.89522 ( 90) hydrogen bonds : bond 0.05691 ( 1056) hydrogen bonds : angle 5.24483 ( 2856) link_BETA1-4 : bond 0.00361 ( 30) link_BETA1-4 : angle 1.09751 ( 90) link_NAG-ASN : bond 0.00410 ( 51) link_NAG-ASN : angle 2.54775 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8212 (mttt) REVERT: A 158 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8272 (mtt180) REVERT: A 215 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: A 394 ASN cc_start: 0.8734 (m-40) cc_final: 0.8263 (m110) REVERT: A 505 TYR cc_start: 0.8500 (m-80) cc_final: 0.7742 (t80) REVERT: A 613 GLN cc_start: 0.8562 (mt0) cc_final: 0.8234 (mt0) REVERT: A 738 CYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7750 (t) REVERT: A 762 GLN cc_start: 0.8371 (tt0) cc_final: 0.8110 (mt0) REVERT: A 869 MET cc_start: 0.8981 (mtt) cc_final: 0.8714 (mtm) REVERT: A 904 TYR cc_start: 0.8468 (m-10) cc_final: 0.7405 (m-10) REVERT: A 947 LYS cc_start: 0.8742 (mttm) cc_final: 0.8142 (mppt) REVERT: A 955 ASN cc_start: 0.7931 (m-40) cc_final: 0.7529 (m110) REVERT: A 957 GLN cc_start: 0.8720 (tt0) cc_final: 0.8413 (tp40) REVERT: B 215 ASP cc_start: 0.7462 (m-30) cc_final: 0.7041 (m-30) REVERT: B 321 GLN cc_start: 0.8576 (mm110) cc_final: 0.8239 (mm110) REVERT: B 394 ASN cc_start: 0.8880 (m-40) cc_final: 0.8529 (m110) REVERT: B 505 TYR cc_start: 0.8543 (m-80) cc_final: 0.7675 (t80) REVERT: B 646 ARG cc_start: 0.8287 (mtm180) cc_final: 0.7911 (mtp180) REVERT: B 738 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7859 (t) REVERT: B 817 PHE cc_start: 0.8477 (t80) cc_final: 0.8126 (t80) REVERT: B 947 LYS cc_start: 0.8568 (mttm) cc_final: 0.7864 (mppt) REVERT: B 955 ASN cc_start: 0.7774 (m-40) cc_final: 0.7534 (m-40) REVERT: B 1073 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7776 (tttm) REVERT: B 1125 ASN cc_start: 0.7938 (p0) cc_final: 0.7430 (p0) REVERT: C 246 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7021 (mtt90) REVERT: C 323 THR cc_start: 0.8369 (p) cc_final: 0.8099 (p) REVERT: C 394 ASN cc_start: 0.8789 (m-40) cc_final: 0.8322 (m110) REVERT: C 505 TYR cc_start: 0.8578 (m-80) cc_final: 0.7696 (t80) REVERT: C 738 CYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7745 (t) REVERT: C 947 LYS cc_start: 0.8440 (mttm) cc_final: 0.7866 (mppt) REVERT: C 1045 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8163 (tttp) outliers start: 42 outliers final: 23 residues processed: 288 average time/residue: 0.6243 time to fit residues: 209.7564 Evaluate side-chains 285 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112539 restraints weight = 47033.699| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.29 r_work: 0.2988 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27678 Z= 0.170 Angle : 0.699 15.676 37827 Z= 0.359 Chirality : 0.050 0.456 4458 Planarity : 0.004 0.047 4755 Dihedral : 6.569 58.593 5258 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 11.69 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3270 helix: 1.26 (0.20), residues: 711 sheet: 0.72 (0.18), residues: 777 loop : -1.81 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 319 TYR 0.023 0.002 TYR B 265 PHE 0.019 0.002 PHE C 133 TRP 0.013 0.002 TRP A 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00404 (27552) covalent geometry : angle 0.66175 (37494) SS BOND : bond 0.00700 ( 45) SS BOND : angle 3.18766 ( 90) hydrogen bonds : bond 0.06500 ( 1056) hydrogen bonds : angle 5.35398 ( 2856) link_BETA1-4 : bond 0.00364 ( 30) link_BETA1-4 : angle 1.09089 ( 90) link_NAG-ASN : bond 0.00411 ( 51) link_NAG-ASN : angle 2.61358 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8291 (mttt) REVERT: A 158 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8319 (mtt180) REVERT: A 215 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: A 394 ASN cc_start: 0.8619 (m-40) cc_final: 0.8164 (m110) REVERT: A 505 TYR cc_start: 0.8346 (m-80) cc_final: 0.7865 (t80) REVERT: A 613 GLN cc_start: 0.8525 (mt0) cc_final: 0.8284 (mt0) REVERT: A 705 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.7986 (t) REVERT: A 762 GLN cc_start: 0.8512 (tt0) cc_final: 0.8137 (mt0) REVERT: A 869 MET cc_start: 0.8982 (mtt) cc_final: 0.8739 (mtm) REVERT: A 904 TYR cc_start: 0.8381 (m-10) cc_final: 0.7373 (m-10) REVERT: A 947 LYS cc_start: 0.8709 (mttm) cc_final: 0.8250 (mppt) REVERT: A 955 ASN cc_start: 0.7920 (m-40) cc_final: 0.7486 (m110) REVERT: A 957 GLN cc_start: 0.8687 (tt0) cc_final: 0.8409 (tp40) REVERT: B 321 GLN cc_start: 0.8605 (mm110) cc_final: 0.8316 (mm110) REVERT: B 394 ASN cc_start: 0.8764 (m-40) cc_final: 0.8469 (m110) REVERT: B 505 TYR cc_start: 0.8395 (m-80) cc_final: 0.7797 (t80) REVERT: B 646 ARG cc_start: 0.8423 (mtm180) cc_final: 0.8056 (mtp180) REVERT: B 660 TYR cc_start: 0.8785 (m-80) cc_final: 0.8561 (m-80) REVERT: B 661 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: B 738 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7481 (t) REVERT: B 817 PHE cc_start: 0.8509 (t80) cc_final: 0.8112 (t80) REVERT: B 947 LYS cc_start: 0.8575 (mttm) cc_final: 0.8007 (mppt) REVERT: B 955 ASN cc_start: 0.7763 (m-40) cc_final: 0.7517 (m-40) REVERT: B 983 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7386 (ptt180) REVERT: B 1073 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7756 (tttm) REVERT: B 1125 ASN cc_start: 0.7984 (p0) cc_final: 0.7541 (p0) REVERT: C 246 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7229 (mtt90) REVERT: C 323 THR cc_start: 0.8404 (p) cc_final: 0.8145 (p) REVERT: C 357 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8056 (tpp-160) REVERT: C 394 ASN cc_start: 0.8661 (m-40) cc_final: 0.8340 (m110) REVERT: C 505 TYR cc_start: 0.8427 (m-80) cc_final: 0.7840 (t80) REVERT: C 738 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7411 (t) REVERT: C 947 LYS cc_start: 0.8353 (mttm) cc_final: 0.7918 (mppt) REVERT: C 1045 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8108 (tttp) outliers start: 50 outliers final: 35 residues processed: 291 average time/residue: 0.6246 time to fit residues: 211.9368 Evaluate side-chains 303 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 658 ASN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114905 restraints weight = 51406.147| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.31 r_work: 0.3002 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27678 Z= 0.130 Angle : 0.638 14.127 37827 Z= 0.325 Chirality : 0.047 0.412 4458 Planarity : 0.004 0.050 4755 Dihedral : 6.441 58.043 5258 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.25 % Allowed : 12.21 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3270 helix: 1.41 (0.20), residues: 711 sheet: 0.75 (0.18), residues: 777 loop : -1.77 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.018 0.001 TYR C 265 PHE 0.016 0.001 PHE A 643 TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00293 (27552) covalent geometry : angle 0.60290 (37494) SS BOND : bond 0.00544 ( 45) SS BOND : angle 2.75752 ( 90) hydrogen bonds : bond 0.05536 ( 1056) hydrogen bonds : angle 5.22558 ( 2856) link_BETA1-4 : bond 0.00370 ( 30) link_BETA1-4 : angle 1.08994 ( 90) link_NAG-ASN : bond 0.00397 ( 51) link_NAG-ASN : angle 2.52370 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8291 (mtt180) REVERT: A 215 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: A 394 ASN cc_start: 0.8614 (m-40) cc_final: 0.8180 (m110) REVERT: A 505 TYR cc_start: 0.8329 (m-80) cc_final: 0.7865 (t80) REVERT: A 603 ASN cc_start: 0.8645 (t0) cc_final: 0.8338 (p0) REVERT: A 613 GLN cc_start: 0.8498 (mt0) cc_final: 0.8248 (mt0) REVERT: A 660 TYR cc_start: 0.8774 (m-80) cc_final: 0.8534 (m-80) REVERT: A 705 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.7968 (t) REVERT: A 738 CYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7519 (t) REVERT: A 762 GLN cc_start: 0.8359 (tt0) cc_final: 0.8061 (mt0) REVERT: A 869 MET cc_start: 0.8943 (mtt) cc_final: 0.8669 (mtm) REVERT: A 904 TYR cc_start: 0.8409 (m-10) cc_final: 0.7415 (m-10) REVERT: A 947 LYS cc_start: 0.8637 (mttm) cc_final: 0.8208 (mppt) REVERT: A 955 ASN cc_start: 0.7878 (m-40) cc_final: 0.7461 (m110) REVERT: A 957 GLN cc_start: 0.8708 (tt0) cc_final: 0.8423 (tp40) REVERT: B 215 ASP cc_start: 0.7392 (m-30) cc_final: 0.7045 (m-30) REVERT: B 321 GLN cc_start: 0.8589 (mm110) cc_final: 0.8312 (mm110) REVERT: B 394 ASN cc_start: 0.8742 (m-40) cc_final: 0.8461 (m110) REVERT: B 505 TYR cc_start: 0.8386 (m-80) cc_final: 0.7824 (t80) REVERT: B 646 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7945 (mtp180) REVERT: B 660 TYR cc_start: 0.8797 (m-80) cc_final: 0.8590 (m-80) REVERT: B 738 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 817 PHE cc_start: 0.8477 (t80) cc_final: 0.8114 (t80) REVERT: B 882 ILE cc_start: 0.8724 (pt) cc_final: 0.8438 (mt) REVERT: B 947 LYS cc_start: 0.8514 (mttm) cc_final: 0.7972 (mppt) REVERT: B 955 ASN cc_start: 0.7728 (m-40) cc_final: 0.7489 (m-40) REVERT: B 1017 GLU cc_start: 0.7909 (tt0) cc_final: 0.7683 (mt-10) REVERT: B 1073 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: B 1125 ASN cc_start: 0.7937 (p0) cc_final: 0.7490 (p0) REVERT: C 66 HIS cc_start: 0.7765 (m90) cc_final: 0.7411 (m-70) REVERT: C 246 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7246 (mtt90) REVERT: C 323 THR cc_start: 0.8391 (p) cc_final: 0.8130 (p) REVERT: C 394 ASN cc_start: 0.8671 (m-40) cc_final: 0.8257 (m110) REVERT: C 505 TYR cc_start: 0.8434 (m-80) cc_final: 0.7848 (t80) REVERT: C 603 ASN cc_start: 0.8492 (t0) cc_final: 0.8078 (p0) REVERT: C 738 CYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7536 (t) REVERT: C 947 LYS cc_start: 0.8339 (mttm) cc_final: 0.7908 (mppt) REVERT: C 1045 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8086 (tttp) outliers start: 36 outliers final: 23 residues processed: 280 average time/residue: 0.5897 time to fit residues: 193.5598 Evaluate side-chains 285 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 231 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 151 optimal weight: 0.0370 chunk 62 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 563 GLN A 954 GLN B 99 ASN B 658 ASN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113170 restraints weight = 56119.156| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.44 r_work: 0.2974 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 27678 Z= 0.161 Angle : 0.683 14.786 37827 Z= 0.350 Chirality : 0.049 0.435 4458 Planarity : 0.004 0.045 4755 Dihedral : 6.517 59.202 5258 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.74 % Allowed : 11.76 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3270 helix: 1.31 (0.20), residues: 711 sheet: 0.73 (0.18), residues: 777 loop : -1.80 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 319 TYR 0.023 0.002 TYR B 265 PHE 0.018 0.002 PHE A 643 TRP 0.011 0.002 TRP A 152 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00381 (27552) covalent geometry : angle 0.64680 (37494) SS BOND : bond 0.00662 ( 45) SS BOND : angle 3.08835 ( 90) hydrogen bonds : bond 0.06286 ( 1056) hydrogen bonds : angle 5.31644 ( 2856) link_BETA1-4 : bond 0.00351 ( 30) link_BETA1-4 : angle 1.07989 ( 90) link_NAG-ASN : bond 0.00400 ( 51) link_NAG-ASN : angle 2.56376 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10605.23 seconds wall clock time: 180 minutes 30.32 seconds (10830.32 seconds total)