Starting phenix.real_space_refine on Sun Jul 5 11:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ybm_33726/07_2026/7ybm_33726.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17439 2.51 5 N 4416 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27456 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.76, per 1000 atoms: 0.21 Number of scatterers: 27456 At special positions: 0 Unit cell: (142.31, 150.87, 196.88, 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 114 16.00 O 5487 8.00 N 4416 7.00 C 17439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 343 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 47 sheets defined 26.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.190A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.755A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.925A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.541A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.909A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.730A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.577A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.860A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.703A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.720A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.715A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.871A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.754A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.321A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.534A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.704A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.806A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.648A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.092A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.910A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.631A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.608A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.074A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.771A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.805A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.683A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 939 removed outlier: 3.668A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.328A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.319A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 94 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 43 current: chain 'B' and resid 538 through 543 removed outlier: 3.549A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 547 current: chain 'B' and resid 573 through 577 removed outlier: 5.333A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.506A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.147A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.887A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.295A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.852A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.798A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 728 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.395A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.551A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 64 current: chain 'B' and resid 187 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 187 through 189 current: chain 'B' and resid 200 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.504A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.975A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.570A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.607A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.554A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 718 through 728 current: chain 'B' and resid 1059 through 1069 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.534A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.543A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.559A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.297A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.937A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.772A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (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 654 through 655 removed outlier: 3.601A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1076 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.597A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 910 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8549 1.34 - 1.46: 7183 1.46 - 1.59: 12181 1.59 - 1.71: 2 1.71 - 1.83: 144 Bond restraints: 28059 Sorted by residual: bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.12e-02 7.97e+03 1.36e+01 bond pdb=" CB PRO B 589 " pdb=" CG PRO B 589 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.74e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C5 MAN U 3 " pdb=" O5 MAN U 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" C5 MAN J 3 " pdb=" O5 MAN J 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 28054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 37404 2.36 - 4.72: 666 4.72 - 7.09: 68 7.09 - 9.45: 10 9.45 - 11.81: 3 Bond angle restraints: 38151 Sorted by residual: angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.46e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.31 110.41 -7.10 8.90e-01 1.26e+00 6.37e+01 angle pdb=" CA PRO B 589 " pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.27e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.27 110.23 -6.96 9.00e-01 1.23e+00 5.98e+01 angle pdb=" N PRO B 899 " pdb=" CA PRO B 899 " pdb=" CB PRO B 899 " ideal model delta sigma weight residual 103.51 110.05 -6.54 9.60e-01 1.09e+00 4.65e+01 ... (remaining 38146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14549 17.98 - 35.96: 1007 35.96 - 53.95: 189 53.95 - 71.93: 38 71.93 - 89.91: 27 Dihedral angle restraints: 15810 sinusoidal: 6177 harmonic: 9633 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.39 81.39 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -159.80 73.80 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 15807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 4624 0.240 - 0.479: 11 0.479 - 0.719: 0 0.719 - 0.959: 1 0.959 - 1.198: 1 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4634 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " 0.094 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO B 589 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.004 2.00e-02 2.50e+03 3.86e-02 1.87e+01 pdb=" CG ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 589 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.055 5.00e-02 4.00e+02 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 416 2.65 - 3.22: 25520 3.22 - 3.78: 40434 3.78 - 4.34: 55053 4.34 - 4.90: 90004 Nonbonded interactions: 211427 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.092 3.040 nonbonded pdb=" OE2 GLU B 988 " pdb=" OG SER C 383 " model vdw 2.159 3.040 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.164 3.040 nonbonded pdb=" O ALA B 924 " pdb=" ND2 ASN B 928 " model vdw 2.170 3.120 nonbonded pdb=" OG SER A 383 " pdb=" OE2 GLU C 988 " model vdw 2.170 3.040 ... (remaining 211422 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 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 : 0.004 0.148 28211 Z= 0.227 Angle : 0.851 20.188 38568 Z= 0.437 Chirality : 0.052 1.198 4637 Planarity : 0.005 0.134 4770 Dihedral : 13.072 89.908 9495 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.07 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3267 helix: 1.63 (0.20), residues: 747 sheet: -0.37 (0.22), residues: 555 loop : -1.28 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.017 0.001 TYR B1138 PHE 0.024 0.001 PHE C 275 TRP 0.012 0.001 TRP B 633 HIS 0.021 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 (28059) covalent geometry : angle 0.77034 / 0.42 (38151) SS BOND : bond 0.00303 / 0.22 ( 39) SS BOND : angle 1.20240 / 0.88 ( 78) hydrogen bonds : bond 0.19630 / 12.96 ( 910) hydrogen bonds : angle 7.52109 / 5.25 ( 2493) link_ALPHA1-4 : bond 0.00601 / 0.39 ( 21) link_ALPHA1-4 : angle 1.92162 / 1.33 ( 63) link_BETA1-4 : bond 0.00683 / 0.42 ( 33) link_BETA1-4 : angle 1.60079 / 1.10 ( 99) link_BETA1-6 : bond 0.01071 / 0.54 ( 3) link_BETA1-6 : angle 1.12912 / 0.59 ( 9) link_NAG-ASN : bond 0.00683 / 0.48 ( 56) link_NAG-ASN : angle 5.26762 / 3.41 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.5873 (t) cc_final: 0.5556 (t) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1490 time to fit residues: 56.1049 Evaluate side-chains 157 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 164 ASN A 394 ASN A 437 ASN A 965 GLN B 66 HIS B 146 HIS B 542 ASN B 644 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 66 HIS C 644 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.209270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175718 restraints weight = 44647.063| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.75 r_work: 0.3808 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28211 Z= 0.189 Angle : 0.760 17.856 38568 Z= 0.360 Chirality : 0.047 0.489 4637 Planarity : 0.005 0.069 4770 Dihedral : 4.799 26.045 3543 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 0.80 % Allowed : 5.85 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3267 helix: 1.55 (0.20), residues: 741 sheet: -0.46 (0.21), residues: 594 loop : -1.46 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.026 0.002 TYR A 266 PHE 0.024 0.002 PHE B 906 TRP 0.015 0.001 TRP B 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (28059) covalent geometry : angle 0.68725 / 0.34 (38151) SS BOND : bond 0.00440 / 0.30 ( 39) SS BOND : angle 1.66828 / 1.12 ( 78) hydrogen bonds : bond 0.06300 / 4.10 ( 910) hydrogen bonds : angle 6.11753 / 4.33 ( 2493) link_ALPHA1-4 : bond 0.00449 / 0.28 ( 21) link_ALPHA1-4 : angle 1.76574 / 1.18 ( 63) link_BETA1-4 : bond 0.00383 / 0.23 ( 33) link_BETA1-4 : angle 1.09067 / 0.78 ( 99) link_BETA1-6 : bond 0.00814 / 0.41 ( 3) link_BETA1-6 : angle 0.84148 / 0.43 ( 9) link_NAG-ASN : bond 0.00615 / 0.43 ( 56) link_NAG-ASN : angle 4.71267 / 3.03 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4584 (p-90) cc_final: 0.3980 (p-90) REVERT: A 738 CYS cc_start: 0.6960 (t) cc_final: 0.6564 (t) REVERT: A 878 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 509 ARG cc_start: 0.4131 (ttm170) cc_final: 0.3925 (ttp-170) REVERT: B 546 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8037 (pp) outliers start: 23 outliers final: 16 residues processed: 190 average time/residue: 0.1526 time to fit residues: 48.4872 Evaluate side-chains 161 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 286 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.0470 chunk 133 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 146 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 232 optimal weight: 20.0000 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 965 GLN B 66 HIS B 146 HIS B 185 ASN B 580 GLN C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.207981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173318 restraints weight = 44659.724| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.85 r_work: 0.3827 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28211 Z= 0.167 Angle : 0.711 16.482 38568 Z= 0.333 Chirality : 0.046 0.451 4637 Planarity : 0.004 0.054 4770 Dihedral : 4.697 26.776 3543 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 1.56 % Allowed : 8.69 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3267 helix: 1.62 (0.20), residues: 738 sheet: -0.59 (0.21), residues: 630 loop : -1.46 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.017 0.001 TYR B1067 PHE 0.018 0.002 PHE A 318 TRP 0.014 0.001 TRP C 886 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (28059) covalent geometry : angle 0.64186 / 0.32 (38151) SS BOND : bond 0.00355 / 0.24 ( 39) SS BOND : angle 1.49217 / 0.99 ( 78) hydrogen bonds : bond 0.06085 / 3.96 ( 910) hydrogen bonds : angle 5.84941 / 4.13 ( 2493) link_ALPHA1-4 : bond 0.00624 / 0.39 ( 21) link_ALPHA1-4 : angle 1.46977 / 0.99 ( 63) link_BETA1-4 : bond 0.00442 / 0.28 ( 33) link_BETA1-4 : angle 1.09645 / 0.78 ( 99) link_BETA1-6 : bond 0.00717 / 0.36 ( 3) link_BETA1-6 : angle 1.07148 / 0.64 ( 9) link_NAG-ASN : bond 0.00857 / 0.66 ( 56) link_NAG-ASN : angle 4.46262 / 2.98 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5402 (tp) REVERT: A 738 CYS cc_start: 0.6859 (t) cc_final: 0.6599 (t) REVERT: B 509 ARG cc_start: 0.4282 (ttm170) cc_final: 0.3988 (ttp-170) REVERT: B 546 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8107 (pp) REVERT: C 878 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8391 (tt) outliers start: 45 outliers final: 27 residues processed: 196 average time/residue: 0.1686 time to fit residues: 55.4871 Evaluate side-chains 173 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 199 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN B 146 HIS B 542 ASN C 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.207347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165775 restraints weight = 44458.249| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.28 r_work: 0.3738 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28211 Z= 0.154 Angle : 0.683 14.127 38568 Z= 0.320 Chirality : 0.045 0.436 4637 Planarity : 0.004 0.052 4770 Dihedral : 4.619 25.858 3543 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 1.83 % Allowed : 10.04 % Favored : 88.13 % 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: -0.79 (0.14), residues: 3267 helix: 1.64 (0.20), residues: 738 sheet: -0.52 (0.20), residues: 669 loop : -1.48 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.020 0.001 TYR A 265 PHE 0.017 0.002 PHE B 65 TRP 0.013 0.001 TRP B 353 HIS 0.020 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (28059) covalent geometry : angle 0.62068 / 0.31 (38151) SS BOND : bond 0.00450 / 0.27 ( 39) SS BOND : angle 1.51086 / 1.01 ( 78) hydrogen bonds : bond 0.05847 / 3.80 ( 910) hydrogen bonds : angle 5.70594 / 4.05 ( 2493) link_ALPHA1-4 : bond 0.00549 / 0.34 ( 21) link_ALPHA1-4 : angle 1.49442 / 1.00 ( 63) link_BETA1-4 : bond 0.00407 / 0.26 ( 33) link_BETA1-4 : angle 1.09081 / 0.77 ( 99) link_BETA1-6 : bond 0.00669 / 0.34 ( 3) link_BETA1-6 : angle 1.03756 / 0.65 ( 9) link_NAG-ASN : bond 0.00640 / 0.46 ( 56) link_NAG-ASN : angle 4.13051 / 2.71 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5519 (tp) REVERT: A 738 CYS cc_start: 0.7124 (t) cc_final: 0.6868 (t) REVERT: A 878 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 65 PHE cc_start: 0.5845 (t80) cc_final: 0.5567 (t80) REVERT: B 117 LEU cc_start: 0.3342 (OUTLIER) cc_final: 0.3002 (tt) REVERT: B 509 ARG cc_start: 0.4325 (ttm170) cc_final: 0.3944 (ttp-170) REVERT: B 546 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (pp) REVERT: C 737 ASP cc_start: 0.7834 (t0) cc_final: 0.7583 (p0) REVERT: C 850 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7740 (mp) REVERT: C 878 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (tt) outliers start: 53 outliers final: 32 residues processed: 201 average time/residue: 0.1596 time to fit residues: 55.1689 Evaluate side-chains 176 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 171 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 206 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN B 146 HIS B 542 ASN B 644 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.205044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.171332 restraints weight = 44280.351| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.71 r_work: 0.3788 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28211 Z= 0.187 Angle : 0.711 13.773 38568 Z= 0.334 Chirality : 0.046 0.420 4637 Planarity : 0.004 0.054 4770 Dihedral : 4.686 24.559 3543 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 2.32 % Allowed : 11.25 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3267 helix: 1.54 (0.20), residues: 738 sheet: -0.61 (0.20), residues: 669 loop : -1.56 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.002 PHE C 201 TRP 0.014 0.001 TRP B 353 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (28059) covalent geometry : angle 0.65525 / 0.32 (38151) SS BOND : bond 0.00510 / 0.35 ( 39) SS BOND : angle 1.72732 / 1.18 ( 78) hydrogen bonds : bond 0.06320 / 4.11 ( 910) hydrogen bonds : angle 5.73708 / 4.06 ( 2493) link_ALPHA1-4 : bond 0.00555 / 0.35 ( 21) link_ALPHA1-4 : angle 1.52598 / 1.02 ( 63) link_BETA1-4 : bond 0.00344 / 0.22 ( 33) link_BETA1-4 : angle 1.12430 / 0.78 ( 99) link_BETA1-6 : bond 0.00624 / 0.32 ( 3) link_BETA1-6 : angle 1.11994 / 0.75 ( 9) link_NAG-ASN : bond 0.00612 / 0.42 ( 56) link_NAG-ASN : angle 3.93010 / 2.60 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5356 (tp) REVERT: A 738 CYS cc_start: 0.6899 (t) cc_final: 0.6640 (t) REVERT: A 878 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 850 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7661 (mp) REVERT: C 878 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (tt) outliers start: 67 outliers final: 42 residues processed: 206 average time/residue: 0.1648 time to fit residues: 57.8503 Evaluate side-chains 176 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 264 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 223 optimal weight: 0.0870 chunk 147 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS B 542 ASN B 644 GLN C 542 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.206338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171848 restraints weight = 44495.892| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.79 r_work: 0.3803 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28211 Z= 0.129 Angle : 0.651 13.886 38568 Z= 0.304 Chirality : 0.045 0.407 4637 Planarity : 0.004 0.044 4770 Dihedral : 4.489 24.980 3543 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.04 % Allowed : 12.50 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3267 helix: 1.74 (0.20), residues: 741 sheet: -0.51 (0.21), residues: 609 loop : -1.49 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.016 0.001 TYR A 265 PHE 0.021 0.001 PHE B 201 TRP 0.014 0.001 TRP B 353 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (28059) covalent geometry : angle 0.60125 / 0.29 (38151) SS BOND : bond 0.00321 / 0.22 ( 39) SS BOND : angle 1.43359 / 0.98 ( 78) hydrogen bonds : bond 0.05420 / 3.51 ( 910) hydrogen bonds : angle 5.50553 / 3.92 ( 2493) link_ALPHA1-4 : bond 0.00579 / 0.36 ( 21) link_ALPHA1-4 : angle 1.46182 / 0.99 ( 63) link_BETA1-4 : bond 0.00427 / 0.27 ( 33) link_BETA1-4 : angle 1.02756 / 0.72 ( 99) link_BETA1-6 : bond 0.00627 / 0.32 ( 3) link_BETA1-6 : angle 1.11493 / 0.72 ( 9) link_NAG-ASN : bond 0.00597 / 0.41 ( 56) link_NAG-ASN : angle 3.58449 / 2.39 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5640 (tp) REVERT: A 738 CYS cc_start: 0.7320 (t) cc_final: 0.7108 (t) REVERT: A 878 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 954 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8509 (mm-40) REVERT: B 779 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8366 (tp40) REVERT: C 48 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8299 (mp) REVERT: C 321 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: C 878 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8400 (tt) outliers start: 59 outliers final: 42 residues processed: 208 average time/residue: 0.1573 time to fit residues: 55.3525 Evaluate side-chains 190 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 279 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1011 GLN B 146 HIS B 542 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.203217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.167715 restraints weight = 44140.507| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.77 r_work: 0.3753 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28211 Z= 0.211 Angle : 0.724 14.527 38568 Z= 0.342 Chirality : 0.047 0.398 4637 Planarity : 0.004 0.045 4770 Dihedral : 4.682 23.634 3543 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 2.28 % Allowed : 13.01 % Favored : 84.70 % 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: -1.00 (0.14), residues: 3267 helix: 1.66 (0.20), residues: 723 sheet: -0.75 (0.20), residues: 633 loop : -1.63 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.021 0.002 TYR B1067 PHE 0.021 0.002 PHE B 541 TRP 0.016 0.001 TRP B 353 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (28059) covalent geometry : angle 0.67567 / 0.33 (38151) SS BOND : bond 0.00419 / 0.29 ( 39) SS BOND : angle 1.70860 / 1.15 ( 78) hydrogen bonds : bond 0.06498 / 4.21 ( 910) hydrogen bonds : angle 5.70823 / 4.05 ( 2493) link_ALPHA1-4 : bond 0.00554 / 0.35 ( 21) link_ALPHA1-4 : angle 1.53543 / 1.02 ( 63) link_BETA1-4 : bond 0.00333 / 0.21 ( 33) link_BETA1-4 : angle 1.13933 / 0.79 ( 99) link_BETA1-6 : bond 0.00508 / 0.26 ( 3) link_BETA1-6 : angle 1.20476 / 0.81 ( 9) link_NAG-ASN : bond 0.00602 / 0.42 ( 56) link_NAG-ASN : angle 3.66275 / 2.47 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5733 (tp) REVERT: A 738 CYS cc_start: 0.6825 (t) cc_final: 0.6574 (t) REVERT: A 878 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 201 PHE cc_start: 0.4832 (t80) cc_final: 0.4580 (t80) REVERT: B 779 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8186 (tp40) REVERT: C 321 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: C 850 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7674 (mp) REVERT: C 878 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 66 outliers final: 48 residues processed: 209 average time/residue: 0.1553 time to fit residues: 54.6214 Evaluate side-chains 188 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 101 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 GLN B 146 HIS C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.205123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.171759 restraints weight = 44495.427| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.68 r_work: 0.3803 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28211 Z= 0.128 Angle : 0.653 14.412 38568 Z= 0.306 Chirality : 0.045 0.405 4637 Planarity : 0.004 0.045 4770 Dihedral : 4.464 23.364 3543 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 13.88 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3267 helix: 1.76 (0.20), residues: 741 sheet: -0.64 (0.20), residues: 639 loop : -1.52 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 34 TYR 0.016 0.001 TYR A 265 PHE 0.038 0.001 PHE B 543 TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (28059) covalent geometry : angle 0.60932 / 0.30 (38151) SS BOND : bond 0.00321 / 0.22 ( 39) SS BOND : angle 1.48779 / 1.01 ( 78) hydrogen bonds : bond 0.05362 / 3.48 ( 910) hydrogen bonds : angle 5.43795 / 3.86 ( 2493) link_ALPHA1-4 : bond 0.00615 / 0.38 ( 21) link_ALPHA1-4 : angle 1.47400 / 1.00 ( 63) link_BETA1-4 : bond 0.00473 / 0.30 ( 33) link_BETA1-4 : angle 1.01271 / 0.70 ( 99) link_BETA1-6 : bond 0.00590 / 0.30 ( 3) link_BETA1-6 : angle 1.20016 / 0.79 ( 9) link_NAG-ASN : bond 0.00570 / 0.39 ( 56) link_NAG-ASN : angle 3.33114 / 2.27 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6659 (t) cc_final: 0.6403 (t) REVERT: A 878 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 48 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (mp) REVERT: C 321 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: C 878 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8336 (tt) outliers start: 54 outliers final: 43 residues processed: 191 average time/residue: 0.1477 time to fit residues: 49.4132 Evaluate side-chains 178 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN B 146 HIS C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.204294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168793 restraints weight = 44420.463| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.85 r_work: 0.3786 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28211 Z= 0.126 Angle : 0.641 14.197 38568 Z= 0.302 Chirality : 0.045 0.405 4637 Planarity : 0.004 0.046 4770 Dihedral : 4.373 24.109 3543 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.01 % Allowed : 14.23 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3267 helix: 1.83 (0.20), residues: 741 sheet: -0.77 (0.20), residues: 678 loop : -1.44 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1107 TYR 0.021 0.001 TYR C 170 PHE 0.025 0.001 PHE C 86 TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (28059) covalent geometry : angle 0.59982 / 0.29 (38151) SS BOND : bond 0.00307 / 0.21 ( 39) SS BOND : angle 1.31919 / 0.89 ( 78) hydrogen bonds : bond 0.05193 / 3.38 ( 910) hydrogen bonds : angle 5.32845 / 3.79 ( 2493) link_ALPHA1-4 : bond 0.00560 / 0.35 ( 21) link_ALPHA1-4 : angle 1.49146 / 1.01 ( 63) link_BETA1-4 : bond 0.00399 / 0.25 ( 33) link_BETA1-4 : angle 1.01727 / 0.70 ( 99) link_BETA1-6 : bond 0.00642 / 0.33 ( 3) link_BETA1-6 : angle 1.16752 / 0.74 ( 9) link_NAG-ASN : bond 0.00561 / 0.38 ( 56) link_NAG-ASN : angle 3.22443 / 2.21 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.7187 (t) cc_final: 0.6971 (t) REVERT: A 878 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 779 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8365 (tp40) REVERT: C 48 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 321 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: C 850 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7792 (mp) REVERT: C 878 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 58 outliers final: 47 residues processed: 195 average time/residue: 0.1499 time to fit residues: 50.5554 Evaluate side-chains 189 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 326 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 chunk 269 optimal weight: 8.9990 chunk 308 optimal weight: 0.0010 chunk 142 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 319 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 245 HIS A1088 HIS A1106 GLN B 146 HIS C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.205962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.172025 restraints weight = 44520.125| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.79 r_work: 0.3816 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 28211 Z= 0.106 Angle : 0.611 14.258 38568 Z= 0.288 Chirality : 0.044 0.366 4637 Planarity : 0.004 0.046 4770 Dihedral : 4.191 23.527 3543 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 1.63 % Allowed : 14.68 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3267 helix: 2.02 (0.20), residues: 741 sheet: -0.56 (0.20), residues: 654 loop : -1.36 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.015 0.001 TYR A 265 PHE 0.022 0.001 PHE C 86 TRP 0.016 0.001 TRP B 353 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (28059) covalent geometry : angle 0.57361 / 0.28 (38151) SS BOND : bond 0.00307 / 0.22 ( 39) SS BOND : angle 1.15034 / 0.78 ( 78) hydrogen bonds : bond 0.04460 / 2.92 ( 910) hydrogen bonds : angle 5.10603 / 3.63 ( 2493) link_ALPHA1-4 : bond 0.00595 / 0.37 ( 21) link_ALPHA1-4 : angle 1.45740 / 0.99 ( 63) link_BETA1-4 : bond 0.00438 / 0.28 ( 33) link_BETA1-4 : angle 0.94602 / 0.65 ( 99) link_BETA1-6 : bond 0.00674 / 0.34 ( 3) link_BETA1-6 : angle 1.18419 / 0.72 ( 9) link_NAG-ASN : bond 0.00547 / 0.37 ( 56) link_NAG-ASN : angle 3.01312 / 2.08 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6644 (t) cc_final: 0.6422 (t) REVERT: C 48 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 277 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6497 (mt) REVERT: C 321 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: C 740 MET cc_start: 0.7992 (ttm) cc_final: 0.7711 (ttt) REVERT: C 878 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8275 (tt) outliers start: 47 outliers final: 37 residues processed: 195 average time/residue: 0.1561 time to fit residues: 52.5498 Evaluate side-chains 178 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 250 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 325 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 245 HIS B 146 HIS B 542 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.210958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.172468 restraints weight = 45871.351| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.05 r_work: 0.3712 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 28211 Z= 0.178 Angle : 0.730 59.197 38568 Z= 0.381 Chirality : 0.047 0.929 4637 Planarity : 0.004 0.046 4770 Dihedral : 4.210 29.876 3543 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 1.56 % Allowed : 14.85 % Favored : 83.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3267 helix: 2.01 (0.20), residues: 741 sheet: -0.56 (0.20), residues: 654 loop : -1.36 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.015 0.001 TYR A 265 PHE 0.018 0.001 PHE C 192 TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (28059) covalent geometry : angle 0.69980 / 0.38 (38151) SS BOND : bond 0.00284 / 0.19 ( 39) SS BOND : angle 1.12787 / 0.76 ( 78) hydrogen bonds : bond 0.04575 / 2.99 ( 910) hydrogen bonds : angle 5.10880 / 3.63 ( 2493) link_ALPHA1-4 : bond 0.00674 / 0.42 ( 21) link_ALPHA1-4 : angle 1.49158 / 1.01 ( 63) link_BETA1-4 : bond 0.00464 / 0.29 ( 33) link_BETA1-4 : angle 0.95174 / 0.66 ( 99) link_BETA1-6 : bond 0.00771 / 0.39 ( 3) link_BETA1-6 : angle 1.19685 / 0.73 ( 9) link_NAG-ASN : bond 0.00543 / 0.36 ( 56) link_NAG-ASN : angle 3.01632 / 2.08 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5488.49 seconds wall clock time: 95 minutes 32.68 seconds (5732.68 seconds total)