Starting phenix.real_space_refine on Sat Aug 8 09:12:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3s_72206/08_2026/9q3s_72206.map" } resolution = 3.01 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= 0.045 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 138 5.16 5 C 16647 2.51 5 N 4398 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26619 Number of models: 1 Model: "" Number of chains: 66 Chain: "B" Number of atoms: 1040 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 bond proxies already assigned to first conformer: 1003 Chain: "G" Number of atoms: 3605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 bond proxies already assigned to first conformer: 3582 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} bond proxies already assigned to first conformer: 808 Chain: "h" Number of atoms: 1026 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Conformer: "B" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} bond proxies already assigned to first conformer: 1033 Chain: "l" Number of atoms: 833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} bond proxies already assigned to first conformer: 835 Chain: "C" Number of atoms: 1040 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 bond proxies already assigned to first conformer: 1003 Chain: "A" Number of atoms: 3605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 bond proxies already assigned to first conformer: 3582 Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "E" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} bond proxies already assigned to first conformer: 808 Chain: "d" Number of atoms: 1026 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Conformer: "B" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} bond proxies already assigned to first conformer: 1033 Chain: "e" Number of atoms: 833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} bond proxies already assigned to first conformer: 835 Chain: "J" Number of atoms: 1040 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 128, 1014 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 bond proxies already assigned to first conformer: 1003 Chain: "I" Number of atoms: 3605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 bond proxies already assigned to first conformer: 3582 Chain: "K" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} bond proxies already assigned to first conformer: 808 Chain: "k" Number of atoms: 1026 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Conformer: "B" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} bond proxies already assigned to first conformer: 1033 Chain: "m" Number of atoms: 833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} bond proxies already assigned to first conformer: 835 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 39 residue: pdb=" N ALYS B 601 " occ=0.47 ... (16 atoms not shown) pdb=" NZ BLYS B 601 " occ=0.53 residue: pdb=" N AGLN B 630 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN B 630 " occ=0.40 residue: pdb=" N AASP B 659 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 659 " occ=0.55 residue: pdb=" N ALYS G 121 " occ=0.48 ... (16 atoms not shown) pdb=" NZ BLYS G 121 " occ=0.52 residue: pdb=" N AARG G 166 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG G 166 " occ=0.37 residue: pdb=" N ALYS G 169 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS G 169 " occ=0.48 residue: pdb=" N ASER G 264 " occ=0.44 ... (10 atoms not shown) pdb=" OG BSER G 264 " occ=0.56 residue: pdb=" N AARG G 444 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG G 444 " occ=0.41 residue: pdb=" N ALYS L 54 " occ=0.63 ... (16 atoms not shown) pdb=" NZ BLYS L 54 " occ=0.37 residue: pdb=" N ALYS h 75 " occ=0.33 ... (16 atoms not shown) pdb=" NZ BLYS h 75 " occ=0.67 residue: pdb=" N ALYS l 95C" occ=0.44 ... (16 atoms not shown) pdb=" NZ BLYS l 95C" occ=0.56 residue: pdb=" N ALYS C 601 " occ=0.49 ... (16 atoms not shown) pdb=" NZ BLYS C 601 " occ=0.51 ... (remaining 27 not shown) Time building chain proxies: 7.77, per 1000 atoms: 0.29 Number of scatterers: 26619 At special positions: 0 Unit cell: (194.394, 187.945, 152.014, 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 138 16.00 O 5436 8.00 N 4398 7.00 C 16647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " 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 ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 6 4 " - " MAN 6 5 " " MAN 6 5 " - " MAN 6 6 " " MAN S 4 " - " MAN S 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN j 4 " - " MAN j 5 " " MAN s 4 " - " MAN s 5 " " MAN s 5 " - " MAN s 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 6 3 " - " MAN 6 4 " " MAN 6 7 " - " MAN 6 8 " " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " " BMA s 3 " - " MAN s 4 " " MAN s 7 " - " MAN s 8 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 6 3 " - " MAN 6 7 " " MAN 6 7 " - " MAN 6 9 " " BMA S 3 " - " MAN S 6 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 9 " " BMA j 3 " - " MAN j 6 " " BMA s 3 " - " MAN s 7 " " MAN s 7 " - " MAN s 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 295 " " NAG 2 1 " - " ASN I 301 " " NAG 3 1 " - " ASN I 363 " " NAG 4 1 " - " ASN I 386 " " NAG 5 1 " - " ASN I 392 " " NAG 6 1 " - " ASN I 332 " " NAG 7 1 " - " ASN I 448 " " NAG 8 1 " - " ASN I 276 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 462 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 462 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 462 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG N 1 " - " ASN G 137 " " NAG O 1 " - " ASN G 156 " " NAG P 1 " - " ASN G 160 " " NAG Q 1 " - " ASN G 355 " " NAG R 1 " - " ASN G 197 " " NAG S 1 " - " ASN G 262 " " NAG T 1 " - " ASN G 295 " " NAG U 1 " - " ASN G 301 " " NAG V 1 " - " ASN G 363 " " NAG W 1 " - " ASN G 386 " " NAG X 1 " - " ASN G 392 " " NAG Y 1 " - " ASN G 332 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 276 " " NAG b 1 " - " ASN A 137 " " NAG c 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 160 " " NAG g 1 " - " ASN A 355 " " NAG i 1 " - " ASN A 197 " " NAG j 1 " - " ASN A 262 " " NAG n 1 " - " ASN A 295 " " NAG o 1 " - " ASN A 301 " " NAG p 1 " - " ASN A 363 " " NAG q 1 " - " ASN A 386 " " NAG r 1 " - " ASN A 392 " " NAG s 1 " - " ASN A 332 " " NAG t 1 " - " ASN A 448 " " NAG u 1 " - " ASN A 276 " " NAG v 1 " - " ASN I 137 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 355 " " NAG z 1 " - " ASN I 197 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 67 sheets defined 14.5% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.947A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.520A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 574' Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.654A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.768A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.759A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.842A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.684A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.868A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 386 through 390 removed outlier: 4.517A pdb=" N GLY G 389 " --> pdb=" O ASN G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 463 removed outlier: 4.191A pdb=" N ASN G 462 " --> pdb=" O GLY G 459 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER G 463 " --> pdb=" O SER G 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 459 through 463' Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.520A pdb=" N GLU L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 100D through 100H Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.505A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 596 removed outlier: 3.533A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.767A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 624' Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.761A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.802A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.720A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.868A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 459 through 463 removed outlier: 4.229A pdb=" N ASN A 462 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 463 " --> pdb=" O SER A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 463' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'd' and resid 100D through 100H Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.981A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 574 removed outlier: 3.588A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 576 through 596 removed outlier: 3.824A pdb=" N ALA J 582 " --> pdb=" O ALA J 578 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 removed outlier: 3.673A pdb=" N TRP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 619 through 624' Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 641 through 659 removed outlier: 3.790A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 removed outlier: 3.790A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 101 through 116 removed outlier: 3.840A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 354 removed outlier: 3.818A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.449A pdb=" N GLY I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 463 removed outlier: 4.204A pdb=" N ASN I 462 " --> pdb=" O GLY I 459 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER I 463 " --> pdb=" O SER I 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 459 through 463' Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'k' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'B' and resid 604 through 609 removed outlier: 5.314A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.878A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.826A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.508A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 200 through 203 removed outlier: 5.833A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.836A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N ILE G 294 " --> pdb=" O AARG G 444 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N AARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.418A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.632A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 36 through 38 removed outlier: 6.590A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 88 through 90 removed outlier: 3.596A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.604A pdb=" N LEU L 73 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.720A pdb=" N MET L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.609A pdb=" N ALA L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN L 37 " --> pdb=" O ALA L 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 6 through 7 Processing sheet with id=AB8, first strand: chain 'h' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'h' and resid 58 through 59 removed outlier: 3.526A pdb=" N ASN h 58 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU h 45 " --> pdb=" O SER h 40 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER h 40 " --> pdb=" O LEU h 45 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP h 47 " --> pdb=" O ARG h 38 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP h 34 " --> pdb=" O VAL h 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR h 33 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG h 94 " --> pdb=" O ASP h 100Q" (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 100 through 100A Processing sheet with id=AC2, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.078A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY l 101 " --> pdb=" O TYR l 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR l 86 " --> pdb=" O GLY l 101 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP l 35 " --> pdb=" O ILE l 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 18 through 22 Processing sheet with id=AC4, first strand: chain 'C' and resid 604 through 609 removed outlier: 5.420A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.832A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AC7, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.886A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.871A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ILE A 294 " --> pdb=" O AARG A 444 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N AARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.382A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.706A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'D' and resid 36 through 38 removed outlier: 6.593A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.539A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.737A pdb=" N MET E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.525A pdb=" N ALA E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN E 37 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 11 through 12 removed outlier: 3.553A pdb=" N ILE d 37 " --> pdb=" O TYR d 91 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR d 33 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP d 34 " --> pdb=" O VAL d 51 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY d 49 " --> pdb=" O TRP d 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG d 38 " --> pdb=" O TRP d 47 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP d 47 " --> pdb=" O ARG d 38 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER d 40 " --> pdb=" O LEU d 45 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU d 45 " --> pdb=" O SER d 40 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 11 through 12 removed outlier: 6.563A pdb=" N CYS d 92 " --> pdb=" O TRP d 101 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRP d 101 " --> pdb=" O CYS d 92 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG d 94 " --> pdb=" O ASP d 100Q" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 70 through 72 Processing sheet with id=AE5, first strand: chain 'd' and resid 100 through 100A Processing sheet with id=AE6, first strand: chain 'e' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'e' and resid 18 through 22 Processing sheet with id=AE8, first strand: chain 'e' and resid 45 through 48 removed outlier: 6.522A pdb=" N TRP e 35 " --> pdb=" O ILE e 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 604 through 609 removed outlier: 5.424A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.878A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 86 " --> pdb=" O VAL I 242 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AF3, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.837A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AF5, first strand: chain 'I' and resid 200 through 203 removed outlier: 5.986A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.756A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE I 294 " --> pdb=" O AARG I 444 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N AARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 315 through 322 removed outlier: 6.407A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.685A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'K' and resid 36 through 38 removed outlier: 6.601A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 88 through 90 removed outlier: 3.679A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 9 through 11 removed outlier: 4.082A pdb=" N MET M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA M 84 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AG5, first strand: chain 'M' and resid 34 through 35 Processing sheet with id=AG6, first strand: chain 'M' and resid 48 through 49 Processing sheet with id=AG7, first strand: chain 'k' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'k' and resid 58 through 59 removed outlier: 3.660A pdb=" N TRP k 34 " --> pdb=" O VAL k 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR k 33 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG k 94 " --> pdb=" O ASP k 100Q" (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'k' and resid 70 through 72 Processing sheet with id=AH1, first strand: chain 'k' and resid 100 through 100A Processing sheet with id=AH2, first strand: chain 'm' and resid 10 through 13 removed outlier: 5.992A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'm' and resid 18 through 22 Processing sheet with id=AH4, first strand: chain 'm' and resid 45 through 48 removed outlier: 6.520A pdb=" N TRP m 35 " --> pdb=" O ILE m 47 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 1758 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: 5.57 Time building geometry restraints manager: 2.91 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: 8205 1.34 - 1.47: 7177 1.47 - 1.59: 11638 1.59 - 1.72: 1 1.72 - 1.84: 186 Bond restraints: 27207 Sorted by residual: bond pdb=" N ASP A 141 " pdb=" CA ASP A 141 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.21e+00 bond pdb=" N ASP G 141 " pdb=" CA ASP G 141 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.16e+00 bond pdb=" N ASP I 141 " pdb=" CA ASP I 141 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.07e+00 bond pdb=" N MET G 150 " pdb=" CA MET G 150 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.27e-02 6.20e+03 5.53e+00 bond pdb=" N ASP G 140 " pdb=" CA ASP G 140 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.24e+00 ... (remaining 27202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 35812 1.75 - 3.50: 1020 3.50 - 5.26: 140 5.26 - 7.01: 40 7.01 - 8.76: 14 Bond angle restraints: 37026 Sorted by residual: angle pdb=" C MET I 150 " pdb=" N ARG I 151 " pdb=" CA ARG I 151 " ideal model delta sigma weight residual 122.59 115.65 6.94 1.57e+00 4.06e-01 1.95e+01 angle pdb=" C MET A 150 " pdb=" N ARG A 151 " pdb=" CA ARG A 151 " ideal model delta sigma weight residual 122.82 115.73 7.09 1.68e+00 3.54e-01 1.78e+01 angle pdb=" C MET G 150 " pdb=" N ARG G 151 " pdb=" CA ARG G 151 " ideal model delta sigma weight residual 122.59 116.08 6.51 1.57e+00 4.06e-01 1.72e+01 angle pdb=" N MET I 150 " pdb=" CA MET I 150 " pdb=" C MET I 150 " ideal model delta sigma weight residual 110.41 105.42 4.99 1.23e+00 6.61e-01 1.65e+01 angle pdb=" N MET G 150 " pdb=" CA MET G 150 " pdb=" C MET G 150 " ideal model delta sigma weight residual 110.35 104.91 5.44 1.38e+00 5.25e-01 1.55e+01 ... (remaining 37021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 16247 25.02 - 50.03: 1425 50.03 - 75.05: 303 75.05 - 100.06: 32 100.06 - 125.08: 47 Dihedral angle restraints: 18054 sinusoidal: 8952 harmonic: 9102 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 142.18 -49.18 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 46.31 46.69 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.56 46.56 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 18051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4521 0.164 - 0.327: 27 0.327 - 0.491: 3 0.491 - 0.654: 0 0.654 - 0.818: 3 Chirality restraints: 4554 Sorted by residual: chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 BMA 6 3 " pdb=" O4 NAG 6 2 " pdb=" C2 BMA 6 3 " pdb=" O5 BMA 6 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.49e+03 ... (remaining 4551 not shown) Planarity restraints: 4584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " -0.227 2.00e-02 2.50e+03 1.98e-01 4.89e+02 pdb=" C7 NAG 6 2 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " 0.339 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.209 2.00e-02 2.50e+03 1.81e-01 4.09e+02 pdb=" C7 NAG Y 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.307 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 1 " 0.210 2.00e-02 2.50e+03 1.76e-01 3.89e+02 pdb=" C7 NAG 6 1 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG 6 1 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG 6 1 " -0.295 2.00e-02 2.50e+03 pdb=" O7 NAG 6 1 " -0.006 2.00e-02 2.50e+03 ... (remaining 4581 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8458 2.84 - 3.35: 22049 3.35 - 3.87: 43762 3.87 - 4.38: 51479 4.38 - 4.90: 89202 Nonbonded interactions: 214950 Sorted by model distance: nonbonded pdb=" O ASN A 356 " pdb=" OD1 ASN A 356 " model vdw 2.319 3.040 nonbonded pdb=" O ASN C 543 " pdb=" ND2 ASN C 543 " model vdw 2.380 3.120 nonbonded pdb=" O ASN G 356 " pdb=" OD1 ASN G 356 " model vdw 2.405 3.040 nonbonded pdb=" O4 MAN 6 5 " pdb=" O6 MAN 6 5 " model vdw 2.433 3.040 nonbonded pdb=" O4 MAN Y 5 " pdb=" O6 MAN Y 5 " model vdw 2.444 3.040 ... (remaining 214945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'j' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '7' selection = chain '8' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '6' selection = chain 'Y' selection = chain 's' } ncs_group { reference = (chain 'A' and (resid 31 through 120 or resid 122 through 165 or resid 167 throu \ gh 168 or resid 170 through 263 or resid 265 through 443 or resid 445 through 60 \ 5)) selection = (chain 'G' and (resid 31 through 120 or resid 122 through 165 or resid 167 throu \ gh 168 or resid 170 through 263 or resid 265 through 443 or resid 445 through 60 \ 5)) selection = (chain 'I' and (resid 31 through 120 or resid 122 through 165 or resid 167 throu \ gh 168 or resid 170 through 263 or resid 265 through 443 or resid 445 through 60 \ 5)) } ncs_group { reference = (chain 'B' and (resid 517 through 600 or resid 602 through 629 or resid 631 thro \ ugh 658 or resid 660 through 702)) selection = (chain 'C' and (resid 517 through 600 or resid 602 through 629 or resid 631 thro \ ugh 658 or resid 660 through 702)) selection = (chain 'J' and (resid 517 through 600 or resid 602 through 629 or resid 631 thro \ ugh 658 or resid 660 through 702)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = (chain 'E' and (resid 1 through 53 or resid 55 through 106A)) selection = (chain 'L' and (resid 1 through 53 or resid 55 through 106A)) selection = (chain 'M' and (resid 1 through 53 or resid 55 through 106A)) } ncs_group { reference = chain 'N' selection = chain 'b' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'c' selection = chain 'w' } ncs_group { reference = (chain 'd' and (resid 2 through 74 or resid 76 through 111)) selection = (chain 'h' and (resid 2 through 74 or resid 76 through 111)) selection = (chain 'k' and (resid 2 through 74 or resid 76 through 111)) } ncs_group { reference = (chain 'e' and (resid 6 through 95B or resid 96 through 107)) selection = (chain 'l' and (resid 6 through 95B or resid 96 through 107)) selection = (chain 'm' and (resid 6 through 95B or resid 96 through 107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 26.760 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.067 27399 Z= 0.198 Angle : 0.800 13.816 37557 Z= 0.381 Chirality : 0.052 0.818 4554 Planarity : 0.008 0.198 4521 Dihedral : 19.252 125.079 12105 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.36 % Favored : 93.35 % Rotamer: Outliers : 5.87 % Allowed : 28.08 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.14), residues: 3183 helix: -1.05 (0.28), residues: 387 sheet: -1.59 (0.16), residues: 999 loop : -1.84 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 98 TYR 0.013 0.001 TYR H 100C PHE 0.013 0.001 PHE I 383 TRP 0.040 0.002 TRP h 36 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (27207) covalent geometry : angle 0.70829 / 0.36 (37026) SS BOND : bond 0.00446 / 0.29 ( 45) SS BOND : angle 1.11714 / 0.81 ( 90) hydrogen bonds : bond 0.19981 / 13.20 ( 710) hydrogen bonds : angle 9.29603 / 6.43 ( 1758) link_ALPHA1-2 : bond 0.03819 / 2.58 ( 9) link_ALPHA1-2 : angle 5.29670 / 3.10 ( 27) link_ALPHA1-3 : bond 0.03430 / 1.84 ( 12) link_ALPHA1-3 : angle 3.49890 / 2.07 ( 36) link_ALPHA1-6 : bond 0.03106 / 2.11 ( 9) link_ALPHA1-6 : angle 3.33012 / 2.03 ( 27) link_BETA1-4 : bond 0.01691 / 1.12 ( 54) link_BETA1-4 : angle 3.06516 / 1.88 ( 162) link_NAG-ASN : bond 0.00470 / 0.24 ( 63) link_NAG-ASN : angle 3.49291 / 2.27 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 255 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8912 (mtt) cc_final: 0.8148 (mmm) REVERT: B 543 ASN cc_start: 0.7922 (t0) cc_final: 0.7608 (t0) REVERT: B 575 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7404 (tp40) REVERT: B 619 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 655 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6625 (tptt) REVERT: B 657 GLU cc_start: 0.7465 (tp30) cc_final: 0.6609 (tt0) REVERT: G 46 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7950 (ptpt) REVERT: G 130 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: G 138 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5766 (tt) REVERT: G 153 GLU cc_start: 0.8329 (tp30) cc_final: 0.7773 (tp30) REVERT: G 207 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7599 (mmtm) REVERT: G 377 ASN cc_start: 0.9101 (t0) cc_final: 0.8873 (t0) REVERT: H 1 GLN cc_start: 0.5811 (OUTLIER) cc_final: 0.5525 (mm110) REVERT: H 32 ASN cc_start: 0.5768 (OUTLIER) cc_final: 0.5196 (m-40) REVERT: h 63 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7206 (pt) REVERT: h 82 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6392 (mt) REVERT: C 535 MET cc_start: 0.8997 (mtt) cc_final: 0.8190 (mmm) REVERT: C 655 LYS cc_start: 0.7553 (tptt) cc_final: 0.6570 (tptt) REVERT: A 88 ASN cc_start: 0.8191 (t0) cc_final: 0.7934 (m-40) REVERT: A 130 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: A 138 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.5880 (tt) REVERT: A 153 GLU cc_start: 0.8244 (tp30) cc_final: 0.8012 (tp30) REVERT: A 211 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: E 29 ILE cc_start: 0.8044 (mm) cc_final: 0.7731 (tp) REVERT: d 82 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6538 (mt) REVERT: d 100 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: J 535 MET cc_start: 0.8887 (mtt) cc_final: 0.8099 (mmm) REVERT: J 542 ARG cc_start: 0.8636 (ptt-90) cc_final: 0.8136 (ptt180) REVERT: J 655 LYS cc_start: 0.7602 (tptt) cc_final: 0.6581 (tptt) REVERT: I 130 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: I 153 GLU cc_start: 0.8216 (tp30) cc_final: 0.7919 (tp30) REVERT: I 207 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7703 (mmtm) REVERT: K 1 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5590 (mm110) REVERT: K 75 LYS cc_start: 0.4327 (OUTLIER) cc_final: 0.2969 (pptt) REVERT: k 63 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7110 (pt) REVERT: k 100 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8618 (mt-10) outliers start: 121 outliers final: 92 residues processed: 364 average time/residue: 0.1457 time to fit residues: 87.1629 Evaluate side-chains 364 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 252 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 6 GLN Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain J residue 617 ARG Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 412 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 47 ILE Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 83 GLU Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.0770 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 97 ASN l 34 GLN l 50 ASN C 543 ASN e 34 GLN J 607 ASN I 287 GLN m 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.204410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159373 restraints weight = 169840.995| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 7.01 r_work: 0.2952 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27399 Z= 0.111 Angle : 0.681 9.033 37557 Z= 0.320 Chirality : 0.045 0.305 4554 Planarity : 0.004 0.055 4521 Dihedral : 14.480 112.898 6630 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 5.87 % Allowed : 27.64 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.14), residues: 3183 helix: -0.84 (0.29), residues: 384 sheet: -1.07 (0.16), residues: 984 loop : -1.85 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 298 TYR 0.015 0.001 TYR l 49 PHE 0.016 0.001 PHE A 383 TRP 0.029 0.001 TRP h 36 HIS 0.003 0.001 HIS M 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (27207) covalent geometry : angle 0.62933 / 0.31 (37026) SS BOND : bond 0.00304 / 0.20 ( 45) SS BOND : angle 0.92165 / 0.68 ( 90) hydrogen bonds : bond 0.03684 / 2.38 ( 710) hydrogen bonds : angle 6.45443 / 4.43 ( 1758) link_ALPHA1-2 : bond 0.01000 / 0.67 ( 9) link_ALPHA1-2 : angle 2.29605 / 1.43 ( 27) link_ALPHA1-3 : bond 0.00889 / 0.58 ( 12) link_ALPHA1-3 : angle 1.75875 / 1.15 ( 36) link_ALPHA1-6 : bond 0.01254 / 0.83 ( 9) link_ALPHA1-6 : angle 1.89425 / 1.17 ( 27) link_BETA1-4 : bond 0.00544 / 0.34 ( 54) link_BETA1-4 : angle 1.89497 / 1.23 ( 162) link_NAG-ASN : bond 0.00499 / 0.27 ( 63) link_NAG-ASN : angle 3.03904 / 1.99 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 271 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8867 (mtt) cc_final: 0.8115 (mmm) REVERT: B 543 ASN cc_start: 0.7862 (t0) cc_final: 0.7592 (t0) REVERT: B 619 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 655 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6572 (tptt) REVERT: B 657 GLU cc_start: 0.7184 (tp30) cc_final: 0.6269 (tt0) REVERT: G 129 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8389 (mt) REVERT: G 130 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: G 150 MET cc_start: 0.4665 (OUTLIER) cc_final: 0.4391 (mtp) REVERT: G 153 GLU cc_start: 0.8224 (tp30) cc_final: 0.7804 (tp30) REVERT: G 207 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7541 (mmtm) REVERT: G 377 ASN cc_start: 0.9043 (t0) cc_final: 0.8799 (t0) REVERT: h 63 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7036 (pt) REVERT: C 535 MET cc_start: 0.8989 (mtt) cc_final: 0.8152 (mmm) REVERT: C 655 LYS cc_start: 0.7169 (tptt) cc_final: 0.6211 (tptt) REVERT: C 657 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6506 (tt0) REVERT: A 130 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8804 (mm-40) REVERT: A 150 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6730 (ttm) REVERT: A 153 GLU cc_start: 0.8192 (tp30) cc_final: 0.7936 (tp30) REVERT: A 211 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: A 457 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: d 34 TRP cc_start: 0.7381 (m100) cc_final: 0.6890 (m100) REVERT: d 100 VAL cc_start: 0.8230 (p) cc_final: 0.8028 (m) REVERT: J 530 MET cc_start: 0.8701 (mtp) cc_final: 0.8482 (mtm) REVERT: J 535 MET cc_start: 0.8883 (mtt) cc_final: 0.8084 (mmm) REVERT: J 542 ARG cc_start: 0.8514 (ptt-90) cc_final: 0.8081 (ptt180) REVERT: J 655 LYS cc_start: 0.7242 (tptt) cc_final: 0.6269 (tptt) REVERT: J 657 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6551 (tt0) REVERT: I 130 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8691 (mm-40) REVERT: I 153 GLU cc_start: 0.8188 (tp30) cc_final: 0.7789 (tp30) REVERT: I 207 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7705 (mmtm) REVERT: K 75 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.2693 (pptt) REVERT: k 36 TRP cc_start: 0.8173 (m100) cc_final: 0.7912 (m100) REVERT: k 63 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6899 (pt) outliers start: 122 outliers final: 71 residues processed: 371 average time/residue: 0.1405 time to fit residues: 86.6113 Evaluate side-chains 352 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 412 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 227 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 249 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 287 GLN H 97 ASN C 543 ASN I 377 ASN K 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.201713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.152555 restraints weight = 180169.017| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 8.80 r_work: 0.2878 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27399 Z= 0.143 Angle : 0.700 9.875 37557 Z= 0.325 Chirality : 0.046 0.328 4554 Planarity : 0.004 0.052 4521 Dihedral : 13.727 106.215 6546 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.13 % Favored : 93.64 % Rotamer: Outliers : 5.95 % Allowed : 26.98 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3183 helix: -0.82 (0.29), residues: 387 sheet: -1.00 (0.16), residues: 948 loop : -1.73 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 480 TYR 0.011 0.001 TYR k 33 PHE 0.017 0.001 PHE G 383 TRP 0.022 0.001 TRP A 69 HIS 0.003 0.001 HIS I 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (27207) covalent geometry : angle 0.64361 / 0.31 (37026) SS BOND : bond 0.00451 / 0.29 ( 45) SS BOND : angle 1.05899 / 0.77 ( 90) hydrogen bonds : bond 0.03732 / 2.44 ( 710) hydrogen bonds : angle 5.98140 / 4.11 ( 1758) link_ALPHA1-2 : bond 0.00847 / 0.57 ( 9) link_ALPHA1-2 : angle 2.50558 / 1.48 ( 27) link_ALPHA1-3 : bond 0.00912 / 0.61 ( 12) link_ALPHA1-3 : angle 1.81676 / 1.17 ( 36) link_ALPHA1-6 : bond 0.01121 / 0.74 ( 9) link_ALPHA1-6 : angle 2.12012 / 1.32 ( 27) link_BETA1-4 : bond 0.00507 / 0.32 ( 54) link_BETA1-4 : angle 1.97157 / 1.27 ( 162) link_NAG-ASN : bond 0.00483 / 0.25 ( 63) link_NAG-ASN : angle 3.21057 / 2.15 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 262 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8919 (mtt) cc_final: 0.8120 (mmm) REVERT: B 543 ASN cc_start: 0.7889 (t0) cc_final: 0.7610 (t0) REVERT: B 619 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 655 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6478 (tptt) REVERT: B 657 GLU cc_start: 0.7162 (tp30) cc_final: 0.6226 (tt0) REVERT: G 130 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: G 153 GLU cc_start: 0.8341 (tp30) cc_final: 0.7877 (tp30) REVERT: G 207 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7549 (mmtm) REVERT: G 377 ASN cc_start: 0.9100 (t0) cc_final: 0.8868 (t0) REVERT: h 63 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6912 (pt) REVERT: C 535 MET cc_start: 0.9038 (mtt) cc_final: 0.8155 (mmm) REVERT: C 655 LYS cc_start: 0.7266 (tptt) cc_final: 0.6324 (tptt) REVERT: C 657 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6439 (tt0) REVERT: A 150 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6604 (ttm) REVERT: A 153 GLU cc_start: 0.8225 (tp30) cc_final: 0.7768 (tp30) REVERT: A 211 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: D 1 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.5440 (mm-40) REVERT: d 100 VAL cc_start: 0.8239 (p) cc_final: 0.8027 (m) REVERT: J 535 MET cc_start: 0.8950 (mtt) cc_final: 0.8123 (mmm) REVERT: J 542 ARG cc_start: 0.8541 (ptt-90) cc_final: 0.8119 (ptt180) REVERT: J 655 LYS cc_start: 0.7199 (tptt) cc_final: 0.6256 (tptt) REVERT: J 657 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6509 (tt0) REVERT: I 130 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8739 (mm-40) REVERT: I 153 GLU cc_start: 0.8268 (tp30) cc_final: 0.7986 (tp30) REVERT: I 207 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7667 (mmtm) REVERT: K 75 LYS cc_start: 0.3873 (OUTLIER) cc_final: 0.2578 (pptt) REVERT: k 63 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6841 (pt) outliers start: 124 outliers final: 79 residues processed: 360 average time/residue: 0.1498 time to fit residues: 88.8180 Evaluate side-chains 349 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 412 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 84 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 220 optimal weight: 0.0980 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.203480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157322 restraints weight = 171169.891| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 7.16 r_work: 0.2920 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27399 Z= 0.130 Angle : 0.687 9.739 37557 Z= 0.317 Chirality : 0.045 0.323 4554 Planarity : 0.004 0.052 4521 Dihedral : 13.046 105.630 6535 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 6.28 % Allowed : 27.13 % Favored : 66.59 % 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: -1.95 (0.14), residues: 3183 helix: -0.76 (0.29), residues: 387 sheet: -0.84 (0.16), residues: 948 loop : -1.69 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 38 TYR 0.011 0.001 TYR h 91 PHE 0.018 0.001 PHE H 63 TRP 0.026 0.001 TRP h 36 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (27207) covalent geometry : angle 0.63143 / 0.30 (37026) SS BOND : bond 0.00361 / 0.24 ( 45) SS BOND : angle 0.98265 / 0.71 ( 90) hydrogen bonds : bond 0.03286 / 2.15 ( 710) hydrogen bonds : angle 5.59845 / 3.84 ( 1758) link_ALPHA1-2 : bond 0.00842 / 0.56 ( 9) link_ALPHA1-2 : angle 2.55935 / 1.54 ( 27) link_ALPHA1-3 : bond 0.01014 / 0.68 ( 12) link_ALPHA1-3 : angle 1.80009 / 1.15 ( 36) link_ALPHA1-6 : bond 0.01192 / 0.79 ( 9) link_ALPHA1-6 : angle 2.24728 / 1.39 ( 27) link_BETA1-4 : bond 0.00496 / 0.31 ( 54) link_BETA1-4 : angle 1.91236 / 1.23 ( 162) link_NAG-ASN : bond 0.00480 / 0.23 ( 63) link_NAG-ASN : angle 3.13860 / 2.10 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 261 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8908 (mtt) cc_final: 0.8118 (mmm) REVERT: B 543 ASN cc_start: 0.7814 (t0) cc_final: 0.7538 (t0) REVERT: B 619 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 655 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6478 (tptt) REVERT: B 657 GLU cc_start: 0.7109 (tp30) cc_final: 0.6260 (tt0) REVERT: G 129 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8458 (mt) REVERT: G 130 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: G 153 GLU cc_start: 0.8281 (tp30) cc_final: 0.7734 (tp30) REVERT: G 207 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7547 (mmtm) REVERT: G 377 ASN cc_start: 0.9084 (t0) cc_final: 0.8874 (t0) REVERT: h 63 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6756 (pt) REVERT: C 535 MET cc_start: 0.9001 (mtt) cc_final: 0.8142 (mmm) REVERT: C 655 LYS cc_start: 0.7272 (tptt) cc_final: 0.6344 (tptt) REVERT: C 657 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6437 (tt0) REVERT: A 46 LYS cc_start: 0.8491 (ptpt) cc_final: 0.8167 (ptpt) REVERT: A 150 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6632 (ttm) REVERT: A 153 GLU cc_start: 0.8165 (tp30) cc_final: 0.7709 (tp30) REVERT: A 211 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: A 420 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 457 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: D 1 GLN cc_start: 0.5597 (OUTLIER) cc_final: 0.5376 (mm-40) REVERT: d 34 TRP cc_start: 0.7385 (m100) cc_final: 0.6950 (m100) REVERT: d 100 VAL cc_start: 0.8262 (p) cc_final: 0.8033 (m) REVERT: J 535 MET cc_start: 0.8912 (mtt) cc_final: 0.8100 (mmm) REVERT: J 542 ARG cc_start: 0.8535 (ptt-90) cc_final: 0.8106 (ptt180) REVERT: J 655 LYS cc_start: 0.7166 (tptt) cc_final: 0.6267 (tptt) REVERT: J 657 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6464 (tt0) REVERT: I 130 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8725 (mm-40) REVERT: I 153 GLU cc_start: 0.8196 (tp30) cc_final: 0.7909 (tp30) REVERT: I 207 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7669 (mmtm) REVERT: K 75 LYS cc_start: 0.4026 (OUTLIER) cc_final: 0.2711 (pptt) REVERT: k 63 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6800 (pt) REVERT: k 69 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7302 (tt) REVERT: m 6 GLN cc_start: 0.1920 (OUTLIER) cc_final: 0.0976 (mt0) outliers start: 134 outliers final: 92 residues processed: 370 average time/residue: 0.1514 time to fit residues: 91.8675 Evaluate side-chains 365 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 257 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 261 optimal weight: 4.9990 chunk 220 optimal weight: 0.3980 chunk 248 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 ASN K 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.204143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157793 restraints weight = 178007.927| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 7.31 r_work: 0.2923 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27399 Z= 0.119 Angle : 0.675 10.649 37557 Z= 0.309 Chirality : 0.045 0.327 4554 Planarity : 0.004 0.056 4521 Dihedral : 12.482 105.423 6531 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.19 % Favored : 93.58 % Rotamer: Outliers : 6.02 % Allowed : 27.28 % Favored : 66.70 % 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: -1.81 (0.15), residues: 3183 helix: -0.73 (0.29), residues: 384 sheet: -0.66 (0.16), residues: 999 loop : -1.64 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 38 TYR 0.011 0.001 TYR h 91 PHE 0.014 0.001 PHE I 383 TRP 0.023 0.001 TRP h 36 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (27207) covalent geometry : angle 0.61991 / 0.30 (37026) SS BOND : bond 0.00355 / 0.23 ( 45) SS BOND : angle 0.93282 / 0.68 ( 90) hydrogen bonds : bond 0.03112 / 2.03 ( 710) hydrogen bonds : angle 5.38669 / 3.69 ( 1758) link_ALPHA1-2 : bond 0.00885 / 0.60 ( 9) link_ALPHA1-2 : angle 2.67352 / 1.60 ( 27) link_ALPHA1-3 : bond 0.01138 / 0.77 ( 12) link_ALPHA1-3 : angle 1.86025 / 1.14 ( 36) link_ALPHA1-6 : bond 0.01238 / 0.82 ( 9) link_ALPHA1-6 : angle 2.33881 / 1.44 ( 27) link_BETA1-4 : bond 0.00489 / 0.31 ( 54) link_BETA1-4 : angle 1.87386 / 1.21 ( 162) link_NAG-ASN : bond 0.00457 / 0.23 ( 63) link_NAG-ASN : angle 3.03941 / 2.04 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 269 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8918 (mtt) cc_final: 0.8119 (mmm) REVERT: B 543 ASN cc_start: 0.7814 (t0) cc_final: 0.7544 (t0) REVERT: B 619 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 632 ASP cc_start: 0.7742 (t0) cc_final: 0.7500 (t0) REVERT: B 655 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6529 (tptt) REVERT: B 657 GLU cc_start: 0.7212 (tp30) cc_final: 0.6310 (tt0) REVERT: G 129 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8397 (mt) REVERT: G 130 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: G 153 GLU cc_start: 0.8241 (tp30) cc_final: 0.7701 (tp30) REVERT: G 207 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7552 (mmtm) REVERT: h 63 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6791 (pt) REVERT: C 535 MET cc_start: 0.9027 (mtt) cc_final: 0.8162 (mmm) REVERT: C 655 LYS cc_start: 0.7213 (tptt) cc_final: 0.6359 (tptt) REVERT: C 657 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6443 (tt0) REVERT: A 46 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8220 (ptpt) REVERT: A 150 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6529 (ttm) REVERT: A 153 GLU cc_start: 0.8205 (tp30) cc_final: 0.7791 (tp30) REVERT: A 211 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: A 457 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: E 53 GLN cc_start: 0.7257 (mm-40) cc_final: 0.7042 (mm-40) REVERT: d 34 TRP cc_start: 0.7393 (m100) cc_final: 0.6988 (m100) REVERT: J 535 MET cc_start: 0.8952 (mtt) cc_final: 0.8111 (mmm) REVERT: J 542 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8134 (ptt180) REVERT: J 655 LYS cc_start: 0.7140 (tptt) cc_final: 0.6266 (tptt) REVERT: J 657 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6481 (tt0) REVERT: I 130 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8719 (mm-40) REVERT: I 150 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6102 (mtm) REVERT: I 153 GLU cc_start: 0.8227 (tp30) cc_final: 0.7944 (tp30) REVERT: I 207 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7667 (mmtm) REVERT: K 75 LYS cc_start: 0.4123 (OUTLIER) cc_final: 0.2784 (pptt) REVERT: k 63 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6776 (pt) REVERT: k 69 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7271 (tt) REVERT: m 6 GLN cc_start: 0.2036 (OUTLIER) cc_final: 0.1154 (mt0) outliers start: 127 outliers final: 95 residues processed: 370 average time/residue: 0.1537 time to fit residues: 93.3536 Evaluate side-chains 374 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 264 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 159 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 68 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.205090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.158805 restraints weight = 179100.174| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 7.38 r_work: 0.2943 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27399 Z= 0.110 Angle : 0.656 10.085 37557 Z= 0.301 Chirality : 0.044 0.325 4554 Planarity : 0.004 0.054 4521 Dihedral : 12.000 105.234 6531 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 6.02 % Allowed : 27.50 % Favored : 66.48 % 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: -1.72 (0.15), residues: 3183 helix: -0.67 (0.29), residues: 384 sheet: -0.60 (0.16), residues: 1005 loop : -1.59 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 480 TYR 0.018 0.001 TYR l 49 PHE 0.022 0.001 PHE H 63 TRP 0.025 0.001 TRP h 36 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (27207) covalent geometry : angle 0.60302 / 0.29 (37026) SS BOND : bond 0.00320 / 0.21 ( 45) SS BOND : angle 0.89557 / 0.65 ( 90) hydrogen bonds : bond 0.02928 / 1.91 ( 710) hydrogen bonds : angle 5.21306 / 3.58 ( 1758) link_ALPHA1-2 : bond 0.00908 / 0.62 ( 9) link_ALPHA1-2 : angle 2.74829 / 1.66 ( 27) link_ALPHA1-3 : bond 0.01033 / 0.69 ( 12) link_ALPHA1-3 : angle 2.11721 / 1.33 ( 36) link_ALPHA1-6 : bond 0.01318 / 0.87 ( 9) link_ALPHA1-6 : angle 2.40651 / 1.47 ( 27) link_BETA1-4 : bond 0.00497 / 0.31 ( 54) link_BETA1-4 : angle 1.80606 / 1.16 ( 162) link_NAG-ASN : bond 0.00465 / 0.23 ( 63) link_NAG-ASN : angle 2.89577 / 1.94 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 275 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8890 (mtt) cc_final: 0.8093 (mmm) REVERT: B 543 ASN cc_start: 0.7784 (t0) cc_final: 0.7511 (t0) REVERT: B 632 ASP cc_start: 0.7742 (t0) cc_final: 0.7489 (t0) REVERT: B 655 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6406 (tptt) REVERT: B 657 GLU cc_start: 0.7144 (tp30) cc_final: 0.6245 (tt0) REVERT: G 129 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8331 (mt) REVERT: G 153 GLU cc_start: 0.8238 (tp30) cc_final: 0.7740 (tp30) REVERT: G 207 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7546 (mmtm) REVERT: G 432 GLN cc_start: 0.7611 (mt0) cc_final: 0.7103 (mp10) REVERT: h 63 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6659 (pt) REVERT: C 535 MET cc_start: 0.8989 (mtt) cc_final: 0.8154 (mmm) REVERT: C 655 LYS cc_start: 0.7114 (tptt) cc_final: 0.6275 (tptt) REVERT: C 657 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6315 (tt0) REVERT: A 46 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8207 (ptpt) REVERT: A 49 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8366 (tt0) REVERT: A 150 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6460 (ttm) REVERT: A 153 GLU cc_start: 0.8219 (tp30) cc_final: 0.7810 (tp30) REVERT: A 211 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: A 457 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: D 1 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5450 (mm-40) REVERT: E 53 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6855 (mm-40) REVERT: d 34 TRP cc_start: 0.7329 (m100) cc_final: 0.6946 (m100) REVERT: d 46 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: J 530 MET cc_start: 0.8669 (mtp) cc_final: 0.8448 (mtm) REVERT: J 535 MET cc_start: 0.8902 (mtt) cc_final: 0.8066 (mmm) REVERT: J 542 ARG cc_start: 0.8553 (ptt-90) cc_final: 0.8142 (ptt180) REVERT: J 655 LYS cc_start: 0.7076 (tptt) cc_final: 0.6226 (tptt) REVERT: J 657 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6435 (tt0) REVERT: I 130 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8752 (mm-40) REVERT: I 153 GLU cc_start: 0.8241 (tp30) cc_final: 0.7960 (tp30) REVERT: I 207 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7661 (mmtm) REVERT: K 75 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.2826 (pptt) REVERT: k 63 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6731 (pt) REVERT: k 69 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7282 (tt) REVERT: m 6 GLN cc_start: 0.2085 (OUTLIER) cc_final: 0.1146 (mt0) outliers start: 127 outliers final: 92 residues processed: 375 average time/residue: 0.1507 time to fit residues: 93.0796 Evaluate side-chains 372 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 266 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 202 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 159 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.203331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.153396 restraints weight = 185523.597| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 9.14 r_work: 0.2909 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27399 Z= 0.147 Angle : 0.694 10.659 37557 Z= 0.319 Chirality : 0.046 0.333 4554 Planarity : 0.004 0.053 4521 Dihedral : 11.791 105.360 6516 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.26 % Favored : 93.51 % Rotamer: Outliers : 5.76 % Allowed : 27.68 % Favored : 66.56 % 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: -1.67 (0.15), residues: 3183 helix: -0.69 (0.29), residues: 387 sheet: -0.51 (0.17), residues: 981 loop : -1.57 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 480 TYR 0.018 0.001 TYR l 49 PHE 0.018 0.001 PHE G 383 TRP 0.024 0.001 TRP h 36 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27207) covalent geometry : angle 0.63663 / 0.31 (37026) SS BOND : bond 0.00415 / 0.28 ( 45) SS BOND : angle 1.10368 / 0.81 ( 90) hydrogen bonds : bond 0.03238 / 2.12 ( 710) hydrogen bonds : angle 5.28679 / 3.63 ( 1758) link_ALPHA1-2 : bond 0.00926 / 0.62 ( 9) link_ALPHA1-2 : angle 2.78917 / 1.67 ( 27) link_ALPHA1-3 : bond 0.00948 / 0.64 ( 12) link_ALPHA1-3 : angle 1.94422 / 1.21 ( 36) link_ALPHA1-6 : bond 0.01359 / 0.90 ( 9) link_ALPHA1-6 : angle 2.43901 / 1.50 ( 27) link_BETA1-4 : bond 0.00491 / 0.31 ( 54) link_BETA1-4 : angle 1.91526 / 1.23 ( 162) link_NAG-ASN : bond 0.00465 / 0.23 ( 63) link_NAG-ASN : angle 3.13767 / 2.11 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 262 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8921 (mtt) cc_final: 0.8131 (mmm) REVERT: B 543 ASN cc_start: 0.7805 (t0) cc_final: 0.7544 (t0) REVERT: B 632 ASP cc_start: 0.7790 (t0) cc_final: 0.7545 (t0) REVERT: B 655 LYS cc_start: 0.7066 (mmtt) cc_final: 0.6488 (tptt) REVERT: B 657 GLU cc_start: 0.7228 (tp30) cc_final: 0.6323 (tt0) REVERT: G 129 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8429 (mt) REVERT: G 153 GLU cc_start: 0.8246 (tp30) cc_final: 0.7755 (tp30) REVERT: G 207 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7641 (mmtm) REVERT: h 63 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (pt) REVERT: h 69 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7418 (tt) REVERT: C 535 MET cc_start: 0.9045 (mtt) cc_final: 0.8215 (mmm) REVERT: C 655 LYS cc_start: 0.7261 (tptt) cc_final: 0.6408 (tptt) REVERT: C 657 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6475 (tt0) REVERT: A 46 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8229 (ptpt) REVERT: A 150 MET cc_start: 0.6922 (ttt) cc_final: 0.6554 (ttm) REVERT: A 153 GLU cc_start: 0.8232 (tp30) cc_final: 0.7686 (tp30) REVERT: A 211 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: A 457 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: D 1 GLN cc_start: 0.5666 (OUTLIER) cc_final: 0.5463 (mm-40) REVERT: D 78 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6080 (mt) REVERT: E 53 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6893 (mm-40) REVERT: d 34 TRP cc_start: 0.7424 (m100) cc_final: 0.7025 (m100) REVERT: d 46 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: J 535 MET cc_start: 0.8927 (mtt) cc_final: 0.8093 (mmm) REVERT: J 542 ARG cc_start: 0.8583 (ptt-90) cc_final: 0.8170 (ptt180) REVERT: J 655 LYS cc_start: 0.7145 (tptt) cc_final: 0.6308 (tptt) REVERT: J 657 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6485 (tt0) REVERT: I 130 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8724 (mm-40) REVERT: I 153 GLU cc_start: 0.8220 (tp30) cc_final: 0.7908 (tp30) REVERT: I 207 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7705 (mmtm) REVERT: I 457 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: K 75 LYS cc_start: 0.4155 (OUTLIER) cc_final: 0.2885 (pptt) REVERT: k 63 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6677 (pt) REVERT: k 69 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7093 (tt) REVERT: m 6 GLN cc_start: 0.1975 (OUTLIER) cc_final: 0.1082 (mt0) outliers start: 120 outliers final: 93 residues processed: 358 average time/residue: 0.1405 time to fit residues: 83.9036 Evaluate side-chains 368 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 259 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 92 CYS Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 0 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 288 optimal weight: 20.0000 chunk 248 optimal weight: 0.0170 chunk 212 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 chunk 260 optimal weight: 50.0000 chunk 209 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.201326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154021 restraints weight = 166071.873| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 6.97 r_work: 0.2855 rms_B_bonded: 6.43 restraints_weight: 2.0000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27399 Z= 0.195 Angle : 0.751 13.666 37557 Z= 0.346 Chirality : 0.048 0.595 4554 Planarity : 0.004 0.054 4521 Dihedral : 11.920 106.254 6512 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.49 % Favored : 93.19 % Rotamer: Outliers : 5.98 % Allowed : 27.50 % Favored : 66.52 % 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: -1.72 (0.15), residues: 3183 helix: -0.82 (0.28), residues: 387 sheet: -0.50 (0.17), residues: 960 loop : -1.59 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 480 TYR 0.019 0.002 TYR l 49 PHE 0.023 0.002 PHE G 383 TRP 0.027 0.002 TRP h 36 HIS 0.005 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (27207) covalent geometry : angle 0.68598 / 0.33 (37026) SS BOND : bond 0.00503 / 0.34 ( 45) SS BOND : angle 1.29989 / 0.93 ( 90) hydrogen bonds : bond 0.03594 / 2.36 ( 710) hydrogen bonds : angle 5.43978 / 3.74 ( 1758) link_ALPHA1-2 : bond 0.00888 / 0.59 ( 9) link_ALPHA1-2 : angle 2.76378 / 1.64 ( 27) link_ALPHA1-3 : bond 0.00844 / 0.57 ( 12) link_ALPHA1-3 : angle 1.87581 / 1.16 ( 36) link_ALPHA1-6 : bond 0.01322 / 0.88 ( 9) link_ALPHA1-6 : angle 2.39467 / 1.49 ( 27) link_BETA1-4 : bond 0.00486 / 0.30 ( 54) link_BETA1-4 : angle 2.05022 / 1.31 ( 162) link_NAG-ASN : bond 0.00479 / 0.27 ( 63) link_NAG-ASN : angle 3.59070 / 2.45 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 265 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8991 (mtt) cc_final: 0.8198 (mmm) REVERT: B 543 ASN cc_start: 0.7807 (t0) cc_final: 0.7547 (t0) REVERT: B 619 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 632 ASP cc_start: 0.7836 (t0) cc_final: 0.7584 (t0) REVERT: B 655 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6587 (tptt) REVERT: B 657 GLU cc_start: 0.7330 (tp30) cc_final: 0.6467 (tt0) REVERT: G 129 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8511 (mt) REVERT: G 153 GLU cc_start: 0.8358 (tp30) cc_final: 0.7908 (tp30) REVERT: G 207 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7660 (mmtm) REVERT: h 63 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6796 (pt) REVERT: h 69 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (tt) REVERT: C 535 MET cc_start: 0.9053 (mtt) cc_final: 0.8247 (mmm) REVERT: C 655 LYS cc_start: 0.7458 (tptt) cc_final: 0.6506 (tptt) REVERT: C 657 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6624 (tt0) REVERT: A 46 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8267 (ptpt) REVERT: A 150 MET cc_start: 0.6879 (ttt) cc_final: 0.6457 (ttm) REVERT: A 153 GLU cc_start: 0.8228 (tp30) cc_final: 0.7812 (tp30) REVERT: A 211 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: A 457 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: D 1 GLN cc_start: 0.5725 (OUTLIER) cc_final: 0.5515 (mm-40) REVERT: D 78 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6324 (mt) REVERT: E 53 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7053 (mm-40) REVERT: d 46 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6975 (tt0) REVERT: J 535 MET cc_start: 0.8998 (mtt) cc_final: 0.8149 (mmm) REVERT: J 542 ARG cc_start: 0.8625 (ptt-90) cc_final: 0.8194 (ptt180) REVERT: J 632 ASP cc_start: 0.7990 (t0) cc_final: 0.7783 (t0) REVERT: J 655 LYS cc_start: 0.7398 (tptt) cc_final: 0.6488 (tptt) REVERT: J 657 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6601 (tt0) REVERT: I 130 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: I 153 GLU cc_start: 0.8283 (tp30) cc_final: 0.7993 (tp30) REVERT: I 207 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7677 (mmtm) REVERT: I 457 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: k 63 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6769 (pt) REVERT: k 69 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7279 (tt) REVERT: m 6 GLN cc_start: 0.1777 (OUTLIER) cc_final: 0.0937 (mt0) REVERT: m 87 TYR cc_start: 0.8081 (m-80) cc_final: 0.7817 (m-10) outliers start: 126 outliers final: 92 residues processed: 366 average time/residue: 0.1439 time to fit residues: 87.3743 Evaluate side-chains 372 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 264 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 92 CYS Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 177 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 543 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.202975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155714 restraints weight = 174022.119| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 7.35 r_work: 0.2902 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27399 Z= 0.139 Angle : 0.696 11.691 37557 Z= 0.321 Chirality : 0.046 0.436 4554 Planarity : 0.004 0.054 4521 Dihedral : 11.646 106.463 6510 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.32 % Favored : 93.45 % Rotamer: Outliers : 5.54 % Allowed : 27.86 % Favored : 66.59 % 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: -1.67 (0.15), residues: 3183 helix: -0.75 (0.29), residues: 387 sheet: -0.53 (0.17), residues: 996 loop : -1.55 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 476 TYR 0.019 0.001 TYR l 49 PHE 0.017 0.001 PHE G 383 TRP 0.029 0.001 TRP h 36 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (27207) covalent geometry : angle 0.63681 / 0.31 (37026) SS BOND : bond 0.00442 / 0.28 ( 45) SS BOND : angle 1.09844 / 0.80 ( 90) hydrogen bonds : bond 0.03186 / 2.09 ( 710) hydrogen bonds : angle 5.30957 / 3.65 ( 1758) link_ALPHA1-2 : bond 0.00892 / 0.60 ( 9) link_ALPHA1-2 : angle 2.79116 / 1.69 ( 27) link_ALPHA1-3 : bond 0.00872 / 0.58 ( 12) link_ALPHA1-3 : angle 1.87001 / 1.17 ( 36) link_ALPHA1-6 : bond 0.01392 / 0.92 ( 9) link_ALPHA1-6 : angle 2.17112 / 1.36 ( 27) link_BETA1-4 : bond 0.00486 / 0.30 ( 54) link_BETA1-4 : angle 1.93300 / 1.25 ( 162) link_NAG-ASN : bond 0.00396 / 0.21 ( 63) link_NAG-ASN : angle 3.24087 / 2.19 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 258 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8908 (mtt) cc_final: 0.8117 (mmm) REVERT: B 543 ASN cc_start: 0.7819 (t0) cc_final: 0.7548 (t0) REVERT: B 619 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7561 (mp) REVERT: B 632 ASP cc_start: 0.7811 (t0) cc_final: 0.7536 (t0) REVERT: B 655 LYS cc_start: 0.6992 (mmtt) cc_final: 0.6413 (tptt) REVERT: B 657 GLU cc_start: 0.7164 (tp30) cc_final: 0.6287 (tt0) REVERT: G 129 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8443 (mt) REVERT: G 153 GLU cc_start: 0.8284 (tp30) cc_final: 0.7844 (tp30) REVERT: G 207 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7571 (mmtm) REVERT: h 63 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6590 (pt) REVERT: h 69 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7451 (tt) REVERT: C 535 MET cc_start: 0.8986 (mtt) cc_final: 0.8158 (mmm) REVERT: C 655 LYS cc_start: 0.7296 (tptt) cc_final: 0.6321 (tptt) REVERT: C 657 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6452 (tt0) REVERT: A 46 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8195 (ptpt) REVERT: A 150 MET cc_start: 0.6907 (ttt) cc_final: 0.6469 (ttm) REVERT: A 153 GLU cc_start: 0.8172 (tp30) cc_final: 0.7861 (tp30) REVERT: A 211 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: A 457 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: E 53 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6838 (mm-40) REVERT: d 34 TRP cc_start: 0.7423 (m100) cc_final: 0.6984 (m100) REVERT: d 46 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: J 535 MET cc_start: 0.8963 (mtt) cc_final: 0.8113 (mmm) REVERT: J 542 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8120 (ptt180) REVERT: J 632 ASP cc_start: 0.7795 (t0) cc_final: 0.7589 (t0) REVERT: J 655 LYS cc_start: 0.7226 (tptt) cc_final: 0.6305 (tptt) REVERT: J 657 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6438 (tm-30) REVERT: I 130 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8739 (mm-40) REVERT: I 153 GLU cc_start: 0.8195 (tp30) cc_final: 0.7902 (tp30) REVERT: I 207 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7640 (mmtm) REVERT: I 457 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: k 63 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6620 (pt) REVERT: k 69 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7083 (tt) REVERT: m 6 GLN cc_start: 0.1918 (OUTLIER) cc_final: 0.1023 (mt0) REVERT: m 87 TYR cc_start: 0.7978 (m-80) cc_final: 0.7729 (m-10) outliers start: 114 outliers final: 94 residues processed: 350 average time/residue: 0.1549 time to fit residues: 89.2370 Evaluate side-chains 365 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 257 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 92 CYS Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 302 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 4 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.204046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156494 restraints weight = 184071.274| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 7.46 r_work: 0.2921 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27399 Z= 0.121 Angle : 0.667 11.487 37557 Z= 0.308 Chirality : 0.045 0.379 4554 Planarity : 0.004 0.054 4521 Dihedral : 11.277 106.385 6507 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 5.51 % Allowed : 27.94 % Favored : 66.56 % 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: -1.58 (0.15), residues: 3183 helix: -0.67 (0.29), residues: 387 sheet: -0.39 (0.17), residues: 981 loop : -1.54 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.018 0.001 TYR l 49 PHE 0.015 0.001 PHE I 383 TRP 0.028 0.001 TRP h 36 HIS 0.003 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27207) covalent geometry : angle 0.61116 / 0.30 (37026) SS BOND : bond 0.00376 / 0.24 ( 45) SS BOND : angle 1.02737 / 0.75 ( 90) hydrogen bonds : bond 0.02971 / 1.95 ( 710) hydrogen bonds : angle 5.17529 / 3.57 ( 1758) link_ALPHA1-2 : bond 0.00925 / 0.63 ( 9) link_ALPHA1-2 : angle 2.86345 / 1.74 ( 27) link_ALPHA1-3 : bond 0.00888 / 0.59 ( 12) link_ALPHA1-3 : angle 1.79933 / 1.12 ( 36) link_ALPHA1-6 : bond 0.01329 / 0.88 ( 9) link_ALPHA1-6 : angle 1.96021 / 1.25 ( 27) link_BETA1-4 : bond 0.00488 / 0.31 ( 54) link_BETA1-4 : angle 1.87848 / 1.21 ( 162) link_NAG-ASN : bond 0.00397 / 0.21 ( 63) link_NAG-ASN : angle 3.05819 / 2.07 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 258 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8893 (mtt) cc_final: 0.8116 (mmm) REVERT: B 543 ASN cc_start: 0.7785 (t0) cc_final: 0.7518 (t0) REVERT: B 619 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 632 ASP cc_start: 0.7820 (t0) cc_final: 0.7549 (t0) REVERT: B 655 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6408 (tptt) REVERT: B 657 GLU cc_start: 0.7272 (tp30) cc_final: 0.6353 (tt0) REVERT: G 129 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8372 (mt) REVERT: G 153 GLU cc_start: 0.8235 (tp30) cc_final: 0.7802 (tp30) REVERT: G 207 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7530 (mmtm) REVERT: h 63 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6593 (pt) REVERT: h 69 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7447 (tt) REVERT: C 535 MET cc_start: 0.9022 (mtt) cc_final: 0.8172 (mmm) REVERT: C 655 LYS cc_start: 0.7232 (tptt) cc_final: 0.6275 (tptt) REVERT: C 657 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6420 (tt0) REVERT: A 46 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8246 (ptpt) REVERT: A 150 MET cc_start: 0.6914 (ttt) cc_final: 0.6486 (ttm) REVERT: A 153 GLU cc_start: 0.8173 (tp30) cc_final: 0.7845 (tp30) REVERT: A 211 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: A 457 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: E 53 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6786 (mm-40) REVERT: d 34 TRP cc_start: 0.7371 (m100) cc_final: 0.6967 (m100) REVERT: J 535 MET cc_start: 0.8947 (mtt) cc_final: 0.8113 (mmm) REVERT: J 542 ARG cc_start: 0.8552 (ptt-90) cc_final: 0.8146 (ptt180) REVERT: J 632 ASP cc_start: 0.7840 (t0) cc_final: 0.7625 (t0) REVERT: J 655 LYS cc_start: 0.7174 (tptt) cc_final: 0.6269 (tptt) REVERT: J 657 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6351 (tt0) REVERT: I 130 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (mm-40) REVERT: I 153 GLU cc_start: 0.8209 (tp30) cc_final: 0.7848 (tp30) REVERT: I 207 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7634 (mmtm) REVERT: I 457 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: k 63 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6622 (pt) REVERT: k 69 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7089 (tt) REVERT: m 6 GLN cc_start: 0.1904 (OUTLIER) cc_final: 0.1018 (mt0) REVERT: m 87 TYR cc_start: 0.7986 (m-80) cc_final: 0.7740 (m-10) outliers start: 113 outliers final: 92 residues processed: 345 average time/residue: 0.1460 time to fit residues: 83.2489 Evaluate side-chains 362 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 257 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 92 CYS Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.154562 restraints weight = 178236.906| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 7.44 r_work: 0.2907 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27399 Z= 0.137 Angle : 0.687 12.087 37557 Z= 0.316 Chirality : 0.046 0.385 4554 Planarity : 0.004 0.054 4521 Dihedral : 11.164 106.452 6502 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 5.32 % Allowed : 28.01 % Favored : 66.67 % 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: -1.56 (0.15), residues: 3183 helix: -0.70 (0.29), residues: 387 sheet: -0.35 (0.17), residues: 981 loop : -1.52 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 480 TYR 0.018 0.001 TYR l 49 PHE 0.018 0.001 PHE G 383 TRP 0.026 0.001 TRP h 36 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (27207) covalent geometry : angle 0.62971 / 0.30 (37026) SS BOND : bond 0.00403 / 0.26 ( 45) SS BOND : angle 1.09322 / 0.79 ( 90) hydrogen bonds : bond 0.03120 / 2.05 ( 710) hydrogen bonds : angle 5.20194 / 3.58 ( 1758) link_ALPHA1-2 : bond 0.00939 / 0.63 ( 9) link_ALPHA1-2 : angle 2.89336 / 1.75 ( 27) link_ALPHA1-3 : bond 0.00868 / 0.58 ( 12) link_ALPHA1-3 : angle 1.74783 / 1.09 ( 36) link_ALPHA1-6 : bond 0.01245 / 0.82 ( 9) link_ALPHA1-6 : angle 1.94626 / 1.25 ( 27) link_BETA1-4 : bond 0.00482 / 0.30 ( 54) link_BETA1-4 : angle 1.91973 / 1.23 ( 162) link_NAG-ASN : bond 0.00400 / 0.22 ( 63) link_NAG-ASN : angle 3.16172 / 2.14 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8584.47 seconds wall clock time: 147 minutes 9.06 seconds (8829.06 seconds total)