Starting phenix.real_space_refine on Sun Sep 13 22:56:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zgf_11204/09_2026/6zgf_11204.cif" } resolution = 3.1 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= 0.003 sd= 0.072 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 117 5.16 5 C 16638 2.51 5 N 4218 2.21 5 O 5190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26163 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 Chain: "B" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 Chain: "C" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 chiralities: 2 Chain: "W" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 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 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 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 chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.85, per 1000 atoms: 0.38 Number of scatterers: 26163 At special positions: 0 Unit cell: (140.14, 135.828, 175.714, 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 117 16.00 O 5190 8.00 N 4218 7.00 C 16638 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 2 " " NAG R 1 " - " FUC R 3 " " NAG W 1 " - " FUC W 2 " " NAG b 1 " - " FUC b 3 " " NAG g 1 " - " FUC g 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG A1315 " - " ASN A 343 " " NAG A1316 " - " ASN A 616 " " NAG A1317 " - " ASN A 705 " " NAG A1321 " - " ASN A1070 " " NAG A1328 " - " ASN A 603 " " NAG A1331 " - " ASN A 657 " " NAG B1301 " - " ASN B 17 " " NAG B1304 " - " ASN B 61 " " NAG B1311 " - " ASN B 282 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B 616 " " NAG B1317 " - " ASN B 705 " " NAG B1321 " - " ASN B1070 " " NAG B1328 " - " ASN B 603 " " NAG B1331 " - " ASN B 657 " " NAG C1301 " - " ASN C 17 " " NAG C1304 " - " ASN C 61 " " NAG C1311 " - " ASN C 282 " " NAG C1315 " - " ASN C 343 " " NAG C1316 " - " ASN C 616 " " NAG C1317 " - " ASN C 705 " " NAG C1321 " - " ASN C1070 " " NAG C1328 " - " ASN C 603 " " NAG C1331 " - " ASN C 657 " " NAG D 1 " - " ASN A 30 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 713 " " NAG J 1 " - " ASN A1094 " " NAG K 1 " - " ASN A1130 " " NAG L 1 " - " ASN A 797 " " NAG M 1 " - " ASN A 370 " " NAG N 1 " - " ASN B 30 " " NAG O 1 " - " ASN B 122 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 713 " " NAG T 1 " - " ASN B1094 " " NAG U 1 " - " ASN B1130 " " NAG V 1 " - " ASN B 797 " " NAG W 1 " - " ASN B 370 " " NAG X 1 " - " ASN C 30 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN C 165 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 331 " " NAG c 1 " - " ASN C 713 " " NAG d 1 " - " ASN C1094 " " NAG e 1 " - " ASN C1130 " " NAG f 1 " - " ASN C 797 " " NAG g 1 " - " ASN C 370 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 24.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.544A pdb=" N ALA A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL A 635 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 636' Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 756 through 768 removed outlier: 3.774A pdb=" N ASN A 760 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 779 removed outlier: 3.989A pdb=" N LYS A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 811 Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.693A pdb=" N ASN A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 862 through 877 removed outlier: 3.832A pdb=" N ALA A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 869 " --> pdb=" O MET A 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.871A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 886 " --> pdb=" O THR A 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 886' Processing helix chain 'A' and resid 893 through 904 removed outlier: 3.943A pdb=" N TYR A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 removed outlier: 3.931A pdb=" N LYS A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA A 940 " --> pdb=" O THR A 937 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 941 " --> pdb=" O ALA A 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 937 through 941' Processing helix chain 'A' and resid 945 through 961 removed outlier: 3.885A pdb=" N GLN A 950 " --> pdb=" O ASP A 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 994 " --> pdb=" O ASP A 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 999 " --> pdb=" O GLY A 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1000 " --> pdb=" O ARG A 996 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.544A pdb=" N ALA B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 636' Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 756 through 768 removed outlier: 3.774A pdb=" N ASN B 760 " --> pdb=" O CYS B 756 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 779 removed outlier: 3.990A pdb=" N LYS B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 811 Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.692A pdb=" N ASN B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU B 837 " --> pdb=" O TYR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 862 through 877 removed outlier: 3.831A pdb=" N ALA B 867 " --> pdb=" O ASP B 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 869 " --> pdb=" O MET B 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.870A pdb=" N GLY B 885 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 886 " --> pdb=" O THR B 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 882 through 886' Processing helix chain 'B' and resid 893 through 904 removed outlier: 3.943A pdb=" N TYR B 900 " --> pdb=" O MET B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 936 " --> pdb=" O ASP B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA B 940 " --> pdb=" O THR B 937 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 941 " --> pdb=" O ALA B 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 937 through 941' Processing helix chain 'B' and resid 945 through 961 removed outlier: 3.885A pdb=" N GLN B 950 " --> pdb=" O ASP B 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 951 " --> pdb=" O VAL B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 955 " --> pdb=" O ASN B 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 994 " --> pdb=" O ASP B 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 998 " --> pdb=" O THR B 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 999 " --> pdb=" O GLY B 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B1000 " --> pdb=" O ARG B 996 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B1012 " --> pdb=" O LEU B1008 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B1013 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.557A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.543A pdb=" N ALA C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 636' Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 756 through 768 removed outlier: 3.775A pdb=" N ASN C 760 " --> pdb=" O CYS C 756 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 762 " --> pdb=" O GLN C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 779 removed outlier: 3.990A pdb=" N LYS C 772 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 811 Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.693A pdb=" N ASN C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU C 837 " --> pdb=" O TYR C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 851 Processing helix chain 'C' and resid 862 through 877 removed outlier: 3.831A pdb=" N ALA C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 869 " --> pdb=" O MET C 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 886 removed outlier: 3.870A pdb=" N GLY C 885 " --> pdb=" O TRP C 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 886 " --> pdb=" O THR C 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 882 through 886' Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.942A pdb=" N TYR C 900 " --> pdb=" O MET C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 removed outlier: 3.931A pdb=" N LYS C 929 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 936 " --> pdb=" O ASP C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA C 940 " --> pdb=" O THR C 937 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 941 " --> pdb=" O ALA C 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 937 through 941' Processing helix chain 'C' and resid 945 through 961 removed outlier: 3.886A pdb=" N GLN C 950 " --> pdb=" O ASP C 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 951 " --> pdb=" O VAL C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 994 " --> pdb=" O ASP C 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 998 " --> pdb=" O THR C 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 999 " --> pdb=" O GLY C 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C1012 " --> pdb=" O LEU C1008 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C1013 " --> pdb=" O ILE C1009 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.164A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.346A pdb=" N ASP A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASN A 542 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.084A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (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 595 through 598 removed outlier: 3.912A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 697 through 699 Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.845A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A1098 " --> pdb=" O GLN A1109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN A1109 " --> pdb=" O TRP A1098 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A1100 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1107 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A1102 " --> pdb=" O PHE A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET A1046 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.691A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.642A pdb=" N ILE A 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.165A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.345A pdb=" N ASP B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN B 542 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.085A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.911A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 697 through 699 Processing sheet with id=AD3, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.846A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B1098 " --> pdb=" O GLN B1109 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN B1109 " --> pdb=" O TRP B1098 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B1100 " --> pdb=" O GLU B1107 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B1107 " --> pdb=" O VAL B1100 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B1102 " --> pdb=" O PHE B1105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET B1046 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.690A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N SER C 221 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG C 34 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N LEU C 223 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.165A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.346A pdb=" N ASP C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN C 542 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 595 through 598 removed outlier: 3.912A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.844A pdb=" N THR C1072 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C1098 " --> pdb=" O GLN C1109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C1109 " --> pdb=" O TRP C1098 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C1100 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU C1107 " --> pdb=" O VAL C1100 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN C1102 " --> pdb=" O PHE C1105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET C1046 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.691A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1116 through 1118 853 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4229 1.32 - 1.44: 7573 1.44 - 1.57: 14793 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 26739 Sorted by residual: bond pdb=" C ASN B 713 " pdb=" O ASN B 713 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" C ASN A 713 " pdb=" O ASN A 713 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" C ASN C 713 " pdb=" O ASN C 713 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" N ILE C 790 " pdb=" CA ILE C 790 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.47e+00 bond pdb=" N ILE A 790 " pdb=" CA ILE A 790 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.35e+00 ... (remaining 26734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 34197 1.58 - 3.16: 1725 3.16 - 4.74: 329 4.74 - 6.32: 112 6.32 - 7.89: 36 Bond angle restraints: 36399 Sorted by residual: angle pdb=" C ASN C 370 " pdb=" CA ASN C 370 " pdb=" CB ASN C 370 " ideal model delta sigma weight residual 110.56 103.01 7.55 1.69e+00 3.50e-01 2.00e+01 angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 110.56 103.02 7.54 1.69e+00 3.50e-01 1.99e+01 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 110.56 103.03 7.53 1.69e+00 3.50e-01 1.98e+01 angle pdb=" CA ASN B 331 " pdb=" C ASN B 331 " pdb=" O ASN B 331 " ideal model delta sigma weight residual 122.37 117.26 5.11 1.15e+00 7.56e-01 1.98e+01 angle pdb=" CA ASN C 331 " pdb=" C ASN C 331 " pdb=" O ASN C 331 " ideal model delta sigma weight residual 122.37 117.31 5.06 1.15e+00 7.56e-01 1.94e+01 ... (remaining 36394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14047 17.87 - 35.74: 941 35.74 - 53.61: 165 53.61 - 71.48: 42 71.48 - 89.35: 18 Dihedral angle restraints: 15213 sinusoidal: 5934 harmonic: 9279 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.26 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.26 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.21 49.21 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4401 0.329 - 0.658: 9 0.658 - 0.987: 0 0.987 - 1.317: 0 1.317 - 1.646: 3 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.42e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.33e+02 ... (remaining 4410 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG R 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG H 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG b 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.118 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 443 2.67 - 3.23: 22961 3.23 - 3.78: 35540 3.78 - 4.34: 50563 4.34 - 4.90: 87994 Nonbonded interactions: 197501 Sorted by model distance: nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.214 3.040 ... (remaining 197496 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 156 or resid 158 through 1331)) selection = (chain 'B' and (resid 14 through 156 or resid 158 through 1331)) selection = (chain 'C' and (resid 14 through 156 or resid 158 through 1331)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) } 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: 5.000 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 31.960 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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 : 0.007 0.041 26877 Z= 0.339 Angle : 0.927 11.068 36768 Z= 0.485 Chirality : 0.074 1.646 4413 Planarity : 0.021 0.284 4572 Dihedral : 12.803 89.347 9102 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.76 % Allowed : 7.12 % Favored : 92.13 % 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: -2.49 (0.14), residues: 3129 helix: -1.97 (0.19), residues: 675 sheet: 0.22 (0.20), residues: 714 loop : -2.43 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 901 TYR 0.016 0.002 TYR C 265 PHE 0.016 0.002 PHE C 65 TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.34 (26739) covalent geometry : angle 0.86039 / 0.47 (36399) SS BOND : bond 0.00434 / 0.25 ( 45) SS BOND : angle 1.35956 / 0.90 ( 90) hydrogen bonds : bond 0.17471 / 12.00 ( 847) hydrogen bonds : angle 7.30620 / 5.16 ( 2307) link_BETA1-4 : bond 0.01702 / 1.14 ( 30) link_BETA1-4 : angle 4.22547 / 2.80 ( 90) link_BETA1-6 : bond 0.00489 / 0.23 ( 6) link_BETA1-6 : angle 2.81341 / 1.80 ( 18) link_NAG-ASN : bond 0.01074 / 0.63 ( 57) link_NAG-ASN : angle 3.98829 / 2.56 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 0.882 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 125 ASN cc_start: 0.7005 (m-40) cc_final: 0.6590 (m-40) REVERT: A 210 ILE cc_start: 0.8167 (tp) cc_final: 0.7736 (tp) REVERT: A 398 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: A 755 PHE cc_start: 0.7303 (m-80) cc_final: 0.6961 (m-80) REVERT: A 898 MET cc_start: 0.8507 (mmm) cc_final: 0.8294 (mmm) REVERT: A 953 GLN cc_start: 0.7493 (tp40) cc_final: 0.7228 (tp40) REVERT: B 125 ASN cc_start: 0.7305 (m-40) cc_final: 0.6774 (m-40) REVERT: B 633 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.7487 (m100) REVERT: C 64 TRP cc_start: 0.8286 (t60) cc_final: 0.7989 (t60) REVERT: C 125 ASN cc_start: 0.7411 (m-40) cc_final: 0.7017 (m-40) REVERT: C 365 TYR cc_start: 0.7935 (m-80) cc_final: 0.7676 (m-80) REVERT: C 953 GLN cc_start: 0.7370 (tp40) cc_final: 0.7103 (tp40) outliers start: 21 outliers final: 12 residues processed: 314 average time/residue: 0.1682 time to fit residues: 84.1442 Evaluate side-chains 200 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 734 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097429 restraints weight = 40468.726| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.70 r_work: 0.2804 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26877 Z= 0.169 Angle : 0.742 11.239 36768 Z= 0.358 Chirality : 0.050 0.504 4413 Planarity : 0.005 0.060 4572 Dihedral : 6.178 57.587 3427 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.87 % Allowed : 9.49 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3129 helix: -1.56 (0.19), residues: 690 sheet: 0.12 (0.19), residues: 762 loop : -2.26 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 158 TYR 0.015 0.001 TYR C 265 PHE 0.014 0.002 PHE B 515 TRP 0.011 0.001 TRP A 436 HIS 0.012 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (26739) covalent geometry : angle 0.70727 / 0.35 (36399) SS BOND : bond 0.00485 / 0.25 ( 45) SS BOND : angle 2.21809 / 1.35 ( 90) hydrogen bonds : bond 0.05318 / 3.51 ( 847) hydrogen bonds : angle 5.64356 / 3.94 ( 2307) link_BETA1-4 : bond 0.00915 / 0.59 ( 30) link_BETA1-4 : angle 2.50871 / 1.81 ( 90) link_BETA1-6 : bond 0.00431 / 0.19 ( 6) link_BETA1-6 : angle 1.50448 / 0.99 ( 18) link_NAG-ASN : bond 0.00343 / 0.23 ( 57) link_NAG-ASN : angle 2.38226 / 1.62 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7642 (m-40) cc_final: 0.6964 (m-40) REVERT: A 210 ILE cc_start: 0.7954 (tp) cc_final: 0.7449 (tp) REVERT: A 212 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 755 PHE cc_start: 0.7634 (m-80) cc_final: 0.7069 (m-80) REVERT: A 898 MET cc_start: 0.9031 (mmm) cc_final: 0.8811 (mmm) REVERT: A 953 GLN cc_start: 0.8126 (tp40) cc_final: 0.7755 (tp40) REVERT: B 111 ASP cc_start: 0.8219 (t70) cc_final: 0.7497 (t0) REVERT: B 125 ASN cc_start: 0.7843 (m-40) cc_final: 0.7221 (m-40) REVERT: B 633 TRP cc_start: 0.9371 (OUTLIER) cc_final: 0.7171 (m100) REVERT: C 125 ASN cc_start: 0.7794 (m-40) cc_final: 0.7349 (m-40) REVERT: C 340 GLU cc_start: 0.8740 (mp0) cc_final: 0.8532 (mm-30) REVERT: C 365 TYR cc_start: 0.8181 (m-80) cc_final: 0.7977 (m-80) REVERT: C 474 GLN cc_start: 0.8466 (tt0) cc_final: 0.8125 (tt0) REVERT: C 554 GLU cc_start: 0.7945 (tt0) cc_final: 0.7692 (tt0) outliers start: 52 outliers final: 37 residues processed: 241 average time/residue: 0.1631 time to fit residues: 64.1116 Evaluate side-chains 214 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 205 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1001 GLN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.099349 restraints weight = 53989.175| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.33 r_work: 0.2782 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26877 Z= 0.150 Angle : 0.679 9.636 36768 Z= 0.332 Chirality : 0.048 0.434 4413 Planarity : 0.004 0.057 4572 Dihedral : 6.030 57.253 3421 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.87 % Allowed : 10.39 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.14), residues: 3129 helix: -1.31 (0.20), residues: 699 sheet: 0.32 (0.19), residues: 783 loop : -2.21 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.014 0.001 TYR B1063 PHE 0.014 0.002 PHE A 194 TRP 0.011 0.001 TRP A 436 HIS 0.012 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (26739) covalent geometry : angle 0.65081 / 0.32 (36399) SS BOND : bond 0.00388 / 0.20 ( 45) SS BOND : angle 1.80364 / 1.11 ( 90) hydrogen bonds : bond 0.04534 / 2.99 ( 847) hydrogen bonds : angle 5.24892 / 3.65 ( 2307) link_BETA1-4 : bond 0.00942 / 0.65 ( 30) link_BETA1-4 : angle 2.41338 / 1.78 ( 90) link_BETA1-6 : bond 0.00373 / 0.17 ( 6) link_BETA1-6 : angle 1.40196 / 0.92 ( 18) link_NAG-ASN : bond 0.00251 / 0.17 ( 57) link_NAG-ASN : angle 1.98753 / 1.36 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7613 (m-40) cc_final: 0.6938 (m-40) REVERT: A 210 ILE cc_start: 0.7954 (tp) cc_final: 0.7446 (tp) REVERT: A 212 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7066 (tt) REVERT: A 755 PHE cc_start: 0.7412 (m-80) cc_final: 0.6949 (m-80) REVERT: A 898 MET cc_start: 0.8913 (mmm) cc_final: 0.8644 (mmm) REVERT: A 953 GLN cc_start: 0.7977 (tp40) cc_final: 0.7546 (tp40) REVERT: B 102 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8304 (tpp-160) REVERT: B 125 ASN cc_start: 0.7681 (m-40) cc_final: 0.7131 (m-40) REVERT: B 633 TRP cc_start: 0.9364 (OUTLIER) cc_final: 0.7101 (m100) REVERT: C 102 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8263 (tpp-160) REVERT: C 125 ASN cc_start: 0.7581 (m-40) cc_final: 0.7135 (m-40) REVERT: C 474 GLN cc_start: 0.8330 (tt0) cc_final: 0.7900 (tt0) outliers start: 52 outliers final: 37 residues processed: 244 average time/residue: 0.1569 time to fit residues: 62.1258 Evaluate side-chains 222 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 166 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 285 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A1001 GLN C1001 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100236 restraints weight = 40365.756| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.67 r_work: 0.2933 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26877 Z= 0.141 Angle : 0.642 9.617 36768 Z= 0.316 Chirality : 0.047 0.415 4413 Planarity : 0.004 0.056 4572 Dihedral : 5.777 56.589 3418 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.87 % Allowed : 11.47 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3129 helix: -1.14 (0.20), residues: 699 sheet: 0.30 (0.19), residues: 753 loop : -2.07 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.014 0.001 TYR C1063 PHE 0.013 0.001 PHE B 133 TRP 0.011 0.001 TRP A 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (26739) covalent geometry : angle 0.61746 / 0.31 (36399) SS BOND : bond 0.00531 / 0.31 ( 45) SS BOND : angle 1.60853 / 0.97 ( 90) hydrogen bonds : bond 0.04305 / 2.83 ( 847) hydrogen bonds : angle 5.09097 / 3.54 ( 2307) link_BETA1-4 : bond 0.00901 / 0.62 ( 30) link_BETA1-4 : angle 2.31756 / 1.71 ( 90) link_BETA1-6 : bond 0.00353 / 0.16 ( 6) link_BETA1-6 : angle 1.27968 / 0.84 ( 18) link_NAG-ASN : bond 0.00218 / 0.14 ( 57) link_NAG-ASN : angle 1.77884 / 1.21 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7669 (m-40) cc_final: 0.7088 (m-40) REVERT: A 210 ILE cc_start: 0.8052 (tp) cc_final: 0.7729 (tp) REVERT: A 744 GLU cc_start: 0.7571 (mp0) cc_final: 0.7260 (mp0) REVERT: A 755 PHE cc_start: 0.7582 (m-80) cc_final: 0.7119 (m-80) REVERT: A 898 MET cc_start: 0.9031 (mmm) cc_final: 0.8756 (mmm) REVERT: A 953 GLN cc_start: 0.8299 (tp40) cc_final: 0.7931 (tp40) REVERT: B 102 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8261 (tpp-160) REVERT: B 125 ASN cc_start: 0.7824 (m-40) cc_final: 0.7372 (m-40) REVERT: C 64 TRP cc_start: 0.8536 (t60) cc_final: 0.8307 (t60) REVERT: C 102 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8292 (tpp-160) REVERT: C 125 ASN cc_start: 0.7717 (m-40) cc_final: 0.7316 (m-40) REVERT: C 474 GLN cc_start: 0.8485 (tt0) cc_final: 0.8113 (tt0) REVERT: C 1115 ASN cc_start: 0.8562 (m-40) cc_final: 0.8320 (m110) outliers start: 52 outliers final: 38 residues processed: 228 average time/residue: 0.1569 time to fit residues: 58.3747 Evaluate side-chains 214 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 49 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 308 optimal weight: 0.4980 chunk 224 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100750 restraints weight = 53807.399| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.43 r_work: 0.2896 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26877 Z= 0.130 Angle : 0.617 9.593 36768 Z= 0.304 Chirality : 0.046 0.395 4413 Planarity : 0.004 0.054 4572 Dihedral : 5.523 47.085 3416 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.91 % Allowed : 11.79 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3129 helix: -0.98 (0.20), residues: 687 sheet: 0.45 (0.19), residues: 777 loop : -2.09 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 158 TYR 0.014 0.001 TYR C1063 PHE 0.017 0.001 PHE C 813 TRP 0.011 0.001 TRP A 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (26739) covalent geometry : angle 0.59518 / 0.30 (36399) SS BOND : bond 0.00339 / 0.18 ( 45) SS BOND : angle 1.38984 / 0.84 ( 90) hydrogen bonds : bond 0.04054 / 2.67 ( 847) hydrogen bonds : angle 4.96029 / 3.45 ( 2307) link_BETA1-4 : bond 0.00841 / 0.58 ( 30) link_BETA1-4 : angle 2.21625 / 1.64 ( 90) link_BETA1-6 : bond 0.00390 / 0.19 ( 6) link_BETA1-6 : angle 1.17880 / 0.76 ( 18) link_NAG-ASN : bond 0.00209 / 0.14 ( 57) link_NAG-ASN : angle 1.64784 / 1.12 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7678 (m-40) cc_final: 0.7215 (m-40) REVERT: A 210 ILE cc_start: 0.8087 (tp) cc_final: 0.7792 (tp) REVERT: A 744 GLU cc_start: 0.7440 (mp0) cc_final: 0.7141 (mp0) REVERT: A 755 PHE cc_start: 0.7460 (m-80) cc_final: 0.7078 (m-80) REVERT: A 898 MET cc_start: 0.8937 (mmm) cc_final: 0.8626 (mmm) REVERT: A 953 GLN cc_start: 0.8009 (tp40) cc_final: 0.7673 (tp40) REVERT: B 102 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8218 (tpp-160) REVERT: B 125 ASN cc_start: 0.7791 (m-40) cc_final: 0.7438 (m-40) REVERT: B 633 TRP cc_start: 0.9368 (OUTLIER) cc_final: 0.7303 (m100) REVERT: C 64 TRP cc_start: 0.8444 (t60) cc_final: 0.8223 (t60) REVERT: C 102 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8269 (tpp-160) REVERT: C 125 ASN cc_start: 0.7560 (m-40) cc_final: 0.7276 (m-40) REVERT: C 474 GLN cc_start: 0.8369 (tt0) cc_final: 0.7973 (tt0) outliers start: 53 outliers final: 45 residues processed: 235 average time/residue: 0.1588 time to fit residues: 60.8633 Evaluate side-chains 229 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 159 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 208 optimal weight: 0.0040 chunk 182 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN C1001 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100834 restraints weight = 40512.374| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.69 r_work: 0.2842 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26877 Z= 0.114 Angle : 0.597 9.578 36768 Z= 0.294 Chirality : 0.045 0.374 4413 Planarity : 0.004 0.052 4572 Dihedral : 5.387 46.678 3416 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.16 % Allowed : 11.61 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3129 helix: -0.83 (0.20), residues: 687 sheet: 0.54 (0.19), residues: 771 loop : -2.03 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.014 0.001 TYR A1063 PHE 0.018 0.001 PHE C 813 TRP 0.011 0.001 TRP A 436 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (26739) covalent geometry : angle 0.57677 / 0.29 (36399) SS BOND : bond 0.00294 / 0.15 ( 45) SS BOND : angle 1.25883 / 0.75 ( 90) hydrogen bonds : bond 0.03756 / 2.48 ( 847) hydrogen bonds : angle 4.85745 / 3.37 ( 2307) link_BETA1-4 : bond 0.00817 / 0.57 ( 30) link_BETA1-4 : angle 2.15225 / 1.58 ( 90) link_BETA1-6 : bond 0.00399 / 0.20 ( 6) link_BETA1-6 : angle 1.15796 / 0.75 ( 18) link_NAG-ASN : bond 0.00201 / 0.13 ( 57) link_NAG-ASN : angle 1.56484 / 1.06 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7512 (m-40) cc_final: 0.7069 (m-40) REVERT: A 210 ILE cc_start: 0.8091 (tp) cc_final: 0.7790 (tp) REVERT: A 744 GLU cc_start: 0.7358 (mp0) cc_final: 0.7053 (mp0) REVERT: A 755 PHE cc_start: 0.7451 (m-80) cc_final: 0.7054 (m-80) REVERT: A 898 MET cc_start: 0.8929 (mmm) cc_final: 0.8613 (mmm) REVERT: A 953 GLN cc_start: 0.7969 (tp40) cc_final: 0.7626 (tp40) REVERT: B 102 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8210 (tpp-160) REVERT: B 125 ASN cc_start: 0.7707 (m-40) cc_final: 0.7400 (m-40) REVERT: B 140 PHE cc_start: 0.8504 (p90) cc_final: 0.8281 (p90) REVERT: B 340 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8139 (tm-30) REVERT: B 633 TRP cc_start: 0.9361 (OUTLIER) cc_final: 0.7346 (m100) REVERT: C 64 TRP cc_start: 0.8411 (t60) cc_final: 0.8203 (t60) REVERT: C 102 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8248 (tpp-160) REVERT: C 125 ASN cc_start: 0.7524 (m-40) cc_final: 0.7305 (m-40) REVERT: C 474 GLN cc_start: 0.8303 (tt0) cc_final: 0.7887 (tt0) outliers start: 60 outliers final: 50 residues processed: 237 average time/residue: 0.1626 time to fit residues: 63.3692 Evaluate side-chains 234 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 157 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 313 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN C1001 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100901 restraints weight = 40395.900| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.66 r_work: 0.2890 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26877 Z= 0.193 Angle : 0.661 9.723 36768 Z= 0.329 Chirality : 0.048 0.378 4413 Planarity : 0.004 0.057 4572 Dihedral : 5.601 48.314 3415 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.19 % Allowed : 11.83 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.14), residues: 3129 helix: -0.96 (0.20), residues: 690 sheet: 0.33 (0.20), residues: 747 loop : -2.01 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 158 TYR 0.019 0.002 TYR C 170 PHE 0.016 0.002 PHE B 133 TRP 0.009 0.001 TRP A 436 HIS 0.008 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (26739) covalent geometry : angle 0.64116 / 0.32 (36399) SS BOND : bond 0.00429 / 0.25 ( 45) SS BOND : angle 1.56758 / 0.94 ( 90) hydrogen bonds : bond 0.04807 / 3.19 ( 847) hydrogen bonds : angle 5.03522 / 3.51 ( 2307) link_BETA1-4 : bond 0.00765 / 0.53 ( 30) link_BETA1-4 : angle 2.09828 / 1.54 ( 90) link_BETA1-6 : bond 0.00361 / 0.18 ( 6) link_BETA1-6 : angle 1.25965 / 0.82 ( 18) link_NAG-ASN : bond 0.00201 / 0.12 ( 57) link_NAG-ASN : angle 1.64178 / 1.09 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7784 (m-40) cc_final: 0.7332 (m-40) REVERT: A 210 ILE cc_start: 0.8155 (tp) cc_final: 0.7793 (tp) REVERT: A 744 GLU cc_start: 0.7450 (mp0) cc_final: 0.7141 (mp0) REVERT: A 755 PHE cc_start: 0.7617 (m-80) cc_final: 0.7218 (m-80) REVERT: A 953 GLN cc_start: 0.8239 (tp40) cc_final: 0.7854 (tp40) REVERT: B 102 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8276 (tpp-160) REVERT: B 111 ASP cc_start: 0.8088 (t70) cc_final: 0.7485 (t0) REVERT: B 125 ASN cc_start: 0.8003 (m-40) cc_final: 0.7586 (m-40) REVERT: B 340 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8266 (tm-30) REVERT: B 633 TRP cc_start: 0.9395 (OUTLIER) cc_final: 0.7323 (m100) REVERT: C 102 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8303 (tpp-160) REVERT: C 125 ASN cc_start: 0.7765 (m-40) cc_final: 0.7558 (m-40) REVERT: C 474 GLN cc_start: 0.8444 (tt0) cc_final: 0.8015 (tt0) REVERT: C 750 LEU cc_start: 0.8075 (mt) cc_final: 0.7844 (mp) outliers start: 61 outliers final: 50 residues processed: 228 average time/residue: 0.1626 time to fit residues: 60.7287 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 270 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 196 ASN C1001 GLN C1115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099260 restraints weight = 46721.901| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.86 r_work: 0.2910 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26877 Z= 0.167 Angle : 0.637 9.687 36768 Z= 0.317 Chirality : 0.047 0.372 4413 Planarity : 0.004 0.057 4572 Dihedral : 5.581 47.963 3415 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.16 % Allowed : 12.15 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3129 helix: -0.94 (0.20), residues: 690 sheet: 0.33 (0.20), residues: 747 loop : -2.00 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.015 0.001 TYR C 170 PHE 0.015 0.002 PHE B 133 TRP 0.010 0.001 TRP A 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (26739) covalent geometry : angle 0.61742 / 0.31 (36399) SS BOND : bond 0.00390 / 0.22 ( 45) SS BOND : angle 1.47086 / 0.88 ( 90) hydrogen bonds : bond 0.04500 / 2.98 ( 847) hydrogen bonds : angle 5.00421 / 3.48 ( 2307) link_BETA1-4 : bond 0.00774 / 0.54 ( 30) link_BETA1-4 : angle 2.08231 / 1.53 ( 90) link_BETA1-6 : bond 0.00393 / 0.19 ( 6) link_BETA1-6 : angle 1.19470 / 0.77 ( 18) link_NAG-ASN : bond 0.00173 / 0.11 ( 57) link_NAG-ASN : angle 1.60475 / 1.07 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7600 (m-40) cc_final: 0.7196 (m-40) REVERT: A 210 ILE cc_start: 0.8156 (tp) cc_final: 0.7801 (tp) REVERT: A 744 GLU cc_start: 0.7447 (mp0) cc_final: 0.7131 (mp0) REVERT: A 755 PHE cc_start: 0.7394 (m-80) cc_final: 0.7085 (m-80) REVERT: A 953 GLN cc_start: 0.7995 (tp40) cc_final: 0.7669 (tp40) REVERT: B 102 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8230 (tpp-160) REVERT: B 111 ASP cc_start: 0.7994 (t70) cc_final: 0.7463 (t0) REVERT: B 125 ASN cc_start: 0.7844 (m-40) cc_final: 0.7489 (m-40) REVERT: B 140 PHE cc_start: 0.8546 (p90) cc_final: 0.8304 (p90) REVERT: B 633 TRP cc_start: 0.9369 (OUTLIER) cc_final: 0.7340 (m100) REVERT: C 102 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (tpp-160) REVERT: C 474 GLN cc_start: 0.8347 (tt0) cc_final: 0.8098 (tt0) outliers start: 60 outliers final: 52 residues processed: 227 average time/residue: 0.1643 time to fit residues: 60.6157 Evaluate side-chains 234 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 164 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN C1001 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101364 restraints weight = 51321.922| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.06 r_work: 0.2876 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26877 Z= 0.130 Angle : 0.613 9.645 36768 Z= 0.304 Chirality : 0.046 0.366 4413 Planarity : 0.004 0.054 4572 Dihedral : 5.499 47.547 3415 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.98 % Allowed : 12.26 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3129 helix: -0.85 (0.20), residues: 690 sheet: 0.41 (0.20), residues: 741 loop : -1.97 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.014 0.001 TYR C1063 PHE 0.013 0.001 PHE B 133 TRP 0.011 0.001 TRP A 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (26739) covalent geometry : angle 0.59365 / 0.30 (36399) SS BOND : bond 0.00325 / 0.18 ( 45) SS BOND : angle 1.34191 / 0.80 ( 90) hydrogen bonds : bond 0.04120 / 2.72 ( 847) hydrogen bonds : angle 4.92360 / 3.42 ( 2307) link_BETA1-4 : bond 0.00788 / 0.55 ( 30) link_BETA1-4 : angle 2.05502 / 1.51 ( 90) link_BETA1-6 : bond 0.00407 / 0.20 ( 6) link_BETA1-6 : angle 1.16163 / 0.75 ( 18) link_NAG-ASN : bond 0.00185 / 0.12 ( 57) link_NAG-ASN : angle 1.56639 / 1.05 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7633 (m-40) cc_final: 0.7201 (m-40) REVERT: A 210 ILE cc_start: 0.8115 (tp) cc_final: 0.7756 (tp) REVERT: A 744 GLU cc_start: 0.7413 (mp0) cc_final: 0.7095 (mp0) REVERT: A 755 PHE cc_start: 0.7433 (m-80) cc_final: 0.7085 (m-80) REVERT: A 953 GLN cc_start: 0.8022 (tp40) cc_final: 0.7673 (tp40) REVERT: B 102 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8221 (tpp-160) REVERT: B 111 ASP cc_start: 0.7990 (t70) cc_final: 0.7463 (t0) REVERT: B 125 ASN cc_start: 0.7839 (m-40) cc_final: 0.7472 (m-40) REVERT: B 633 TRP cc_start: 0.9369 (OUTLIER) cc_final: 0.7283 (m100) REVERT: C 102 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8272 (tpp-160) REVERT: C 474 GLN cc_start: 0.8336 (tt0) cc_final: 0.7891 (tt0) outliers start: 55 outliers final: 49 residues processed: 221 average time/residue: 0.1642 time to fit residues: 59.3257 Evaluate side-chains 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1001 GLN C1115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100840 restraints weight = 48594.140| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.99 r_work: 0.2880 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26877 Z= 0.122 Angle : 0.600 9.621 36768 Z= 0.297 Chirality : 0.046 0.360 4413 Planarity : 0.004 0.053 4572 Dihedral : 5.401 47.170 3415 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.98 % Allowed : 12.15 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3129 helix: -0.76 (0.20), residues: 690 sheet: 0.43 (0.20), residues: 741 loop : -1.93 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.014 0.001 TYR C1063 PHE 0.017 0.001 PHE C 813 TRP 0.011 0.001 TRP A 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (26739) covalent geometry : angle 0.58085 / 0.29 (36399) SS BOND : bond 0.00305 / 0.16 ( 45) SS BOND : angle 1.28481 / 0.76 ( 90) hydrogen bonds : bond 0.03909 / 2.58 ( 847) hydrogen bonds : angle 4.84710 / 3.37 ( 2307) link_BETA1-4 : bond 0.00779 / 0.54 ( 30) link_BETA1-4 : angle 2.02364 / 1.48 ( 90) link_BETA1-6 : bond 0.00399 / 0.20 ( 6) link_BETA1-6 : angle 1.14710 / 0.74 ( 18) link_NAG-ASN : bond 0.00182 / 0.12 ( 57) link_NAG-ASN : angle 1.53228 / 1.03 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7762 (m-40) cc_final: 0.7317 (m-40) REVERT: A 210 ILE cc_start: 0.8061 (tp) cc_final: 0.7710 (tp) REVERT: A 744 GLU cc_start: 0.7481 (mp0) cc_final: 0.7147 (mp0) REVERT: A 755 PHE cc_start: 0.7600 (m-80) cc_final: 0.7165 (m-80) REVERT: A 953 GLN cc_start: 0.8232 (tp40) cc_final: 0.7836 (tp40) REVERT: B 102 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8235 (tpp-160) REVERT: B 111 ASP cc_start: 0.8026 (t70) cc_final: 0.7460 (t0) REVERT: B 125 ASN cc_start: 0.7905 (m-40) cc_final: 0.7517 (m-40) REVERT: B 340 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8185 (tm-30) REVERT: B 633 TRP cc_start: 0.9389 (OUTLIER) cc_final: 0.7206 (m100) REVERT: C 102 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8285 (tpp-160) REVERT: C 430 THR cc_start: 0.8585 (m) cc_final: 0.8375 (m) REVERT: C 474 GLN cc_start: 0.8368 (tt0) cc_final: 0.7925 (tt0) REVERT: C 1115 ASN cc_start: 0.8498 (m-40) cc_final: 0.8297 (m110) outliers start: 55 outliers final: 50 residues processed: 223 average time/residue: 0.1702 time to fit residues: 61.8183 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 282 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 118 optimal weight: 0.1980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094474 restraints weight = 43801.309| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.88 r_work: 0.2857 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26877 Z= 0.113 Angle : 0.583 9.596 36768 Z= 0.289 Chirality : 0.045 0.352 4413 Planarity : 0.004 0.050 4572 Dihedral : 5.256 47.012 3415 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.87 % Allowed : 12.41 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3129 helix: -0.62 (0.20), residues: 687 sheet: 0.47 (0.20), residues: 711 loop : -1.85 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.014 0.001 TYR C1063 PHE 0.022 0.001 PHE C 562 TRP 0.011 0.001 TRP A 436 HIS 0.010 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (26739) covalent geometry : angle 0.56476 / 0.28 (36399) SS BOND : bond 0.00278 / 0.15 ( 45) SS BOND : angle 1.21053 / 0.71 ( 90) hydrogen bonds : bond 0.03678 / 2.42 ( 847) hydrogen bonds : angle 4.75449 / 3.30 ( 2307) link_BETA1-4 : bond 0.00750 / 0.52 ( 30) link_BETA1-4 : angle 1.96630 / 1.44 ( 90) link_BETA1-6 : bond 0.00418 / 0.21 ( 6) link_BETA1-6 : angle 1.14594 / 0.74 ( 18) link_NAG-ASN : bond 0.00182 / 0.12 ( 57) link_NAG-ASN : angle 1.47597 / 1.00 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6815.88 seconds wall clock time: 117 minutes 19.07 seconds (7039.07 seconds total)