Starting phenix.real_space_refine on Fri Sep 19 04:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643.map" model { file = "/net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v8l_8643/09_2025/5v8l_8643_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 129 5.16 5 C 14310 2.51 5 N 3784 2.21 5 O 4711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22934 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3545 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "J" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} 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: 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: "T" 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: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "l" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "t" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "y" 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: "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: 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 78 residue: pdb=" C1 NAG P 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 1 " occ=0.00 residue: pdb=" C1 NAG P 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 2 " occ=0.00 residue: pdb=" C1 NAG R 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 1 " occ=0.00 residue: pdb=" C1 NAG R 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 2 " occ=0.00 residue: pdb=" C1 NAG S 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 1 " occ=0.00 residue: pdb=" C1 NAG S 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 2 " occ=0.00 residue: pdb=" C1 BMA S 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA S 3 " occ=0.00 residue: pdb=" C1 NAG T 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 1 " occ=0.00 residue: pdb=" C1 NAG T 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 2 " occ=0.00 residue: pdb=" C1 BMA T 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA T 3 " occ=0.00 residue: pdb=" C1 MAN T 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.00 residue: pdb=" C1 MAN T 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 5 " occ=0.00 ... (remaining 66 not shown) Time building chain proxies: 5.14, per 1000 atoms: 0.22 Number of scatterers: 22934 At special positions: 0 Unit cell: (148.03, 144.1, 171.61, 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 129 16.00 O 4711 8.00 N 3784 7.00 C 14310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.06 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.23 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.20 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.09 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.09 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.17 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.08 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.05 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.12 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.14 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 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 Atom "HETATM21625 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN f 4 " - " MAN f 5 " " MAN g 4 " - " MAN g 5 " " MAN q 4 " - " MAN q 5 " " MAN s 4 " - " MAN s 5 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " MAN t 6 " - " MAN t 7 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 8 " " BMA k 3 " - " MAN k 5 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 8 " " BMA s 3 " - " MAN s 6 " " BMA t 3 " - " MAN t 6 " " MAN t 6 " - " MAN t 8 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " 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 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " 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 t 2 " - " BMA t 3 " " 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 x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN E 637 " " NAG 1 1 " - " ASN F 611 " " NAG 2 1 " - " ASN K 72 " " NAG 3 1 " - " ASN L 72 " " NAG 4 1 " - " ASN M 72 " " NAG A 612 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 642 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 611 " - " ASN C 234 " " NAG C 633 " - " ASN C 339 " " NAG C 634 " - " ASN C 355 " " NAG D 603 " - " ASN D 133 " " NAG D 616 " - " ASN D 234 " " NAG D 638 " - " ASN D 339 " " NAG D 639 " - " ASN D 355 " " NAG D 648 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 133 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 276 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN D 88 " " NAG p 1 " - " ASN D 156 " " NAG q 1 " - " ASN D 160 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 262 " " NAG t 1 " - " ASN D 276 " " NAG u 1 " - " ASN D 295 " " NAG v 1 " - " ASN D 301 " " NAG w 1 " - " ASN D 332 " " NAG x 1 " - " ASN D 363 " " NAG y 1 " - " ASN D 386 " " NAG z 1 " - " ASN D 448 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 871.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 49 sheets defined 23.3% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 removed outlier: 5.630A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.511A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.811A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.362A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.810A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.786A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.634A pdb=" N THR C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.559A pdb=" N VAL D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.619A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.465A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 597 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 650 through 663 Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.813A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 542 through 544 No H-bonds generated for 'chain 'F' and resid 542 through 544' Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 650 through 663 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.613A pdb=" N ASP G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 26 through 32 removed outlier: 5.887A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.066A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 removed outlier: 6.621A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.211A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.702A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 202 removed outlier: 6.838A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.207A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'D' and resid 76 through 77 removed outlier: 7.021A pdb=" N THR D 77 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 56 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.715A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.222A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.384A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.924A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.384A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 304 through 306 Processing sheet with id=AD2, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.390A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE G 33 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.390A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.566A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE H 33 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.449A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE I 33 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.449A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 removed outlier: 4.453A pdb=" N SER J 16 " --> pdb=" O GLY J 82B" (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 82B" --> pdb=" O SER J 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.473A pdb=" N VAL J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP J 50 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.770A pdb=" N CYS J 92 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL J 107 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR J 94 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU J 105 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER J 96 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU J 100O" --> pdb=" O ASP J 100B" (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE J 100D" --> pdb=" O TYR J 100M" (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR J 100M" --> pdb=" O PHE J 100D" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 11 Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.406A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.484A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.434A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU N 33 " --> pdb=" O HIS N 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 10 through 13 853 hydrogen bonds defined for protein. 2022 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: 4.22 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6011 1.33 - 1.46: 6563 1.46 - 1.58: 10649 1.58 - 1.71: 6 1.71 - 1.84: 175 Bond restraints: 23404 Sorted by residual: bond pdb=" CA PHE I 78 " pdb=" C PHE I 78 " ideal model delta sigma weight residual 1.521 1.462 0.059 1.20e-02 6.94e+03 2.46e+01 bond pdb=" CA ILE F 641 " pdb=" C ILE F 641 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.23e-02 6.61e+03 2.38e+01 bond pdb=" C3 MAN t 5 " pdb=" C4 MAN t 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CA PHE H 78 " pdb=" C PHE H 78 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.21e-02 6.83e+03 2.04e+01 bond pdb=" C3 MAN g 5 " pdb=" C4 MAN g 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 23399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 27494 2.53 - 5.07: 3464 5.07 - 7.60: 700 7.60 - 10.13: 93 10.13 - 12.67: 38 Bond angle restraints: 31789 Sorted by residual: angle pdb=" C LYS C 252 " pdb=" N PRO C 253 " pdb=" CA PRO C 253 " ideal model delta sigma weight residual 120.12 131.29 -11.17 1.11e+00 8.12e-01 1.01e+02 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 129.01 -9.45 1.02e+00 9.61e-01 8.58e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 128.83 -9.27 1.02e+00 9.61e-01 8.27e+01 angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 119.85 129.03 -9.18 1.01e+00 9.80e-01 8.26e+01 ... (remaining 31784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 15054 20.34 - 40.67: 536 40.67 - 61.01: 219 61.01 - 81.34: 89 81.34 - 101.68: 65 Dihedral angle restraints: 15963 sinusoidal: 8366 harmonic: 7597 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.44 85.44 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.27 45.27 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual 93.00 136.53 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 15960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.445: 3948 0.445 - 0.890: 26 0.890 - 1.336: 1 1.336 - 1.781: 0 1.781 - 2.226: 2 Chirality restraints: 3977 Sorted by residual: chirality pdb=" C1 MAN U 4 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN g 6 " pdb=" O6 BMA g 3 " pdb=" C2 MAN g 6 " pdb=" O5 MAN g 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN t 6 " pdb=" O6 BMA t 3 " pdb=" C2 MAN t 6 " pdb=" O5 MAN t 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 ... (remaining 3974 not shown) Planarity restraints: 3901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " -0.259 2.00e-02 2.50e+03 3.18e-01 1.26e+03 pdb=" CG ASN C 386 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " 0.511 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.404 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 363 " 0.265 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" CG ASN C 363 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN C 363 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN C 363 " -0.458 2.00e-02 2.50e+03 pdb=" C1 NAG k 1 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 363 " 0.218 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" CG ASN D 363 " -0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN D 363 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN D 363 " -0.492 2.00e-02 2.50e+03 pdb=" C1 NAG x 1 " 0.342 2.00e-02 2.50e+03 ... (remaining 3898 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 63 2.41 - 3.03: 15575 3.03 - 3.65: 33158 3.65 - 4.28: 53138 4.28 - 4.90: 83439 Nonbonded interactions: 185373 Sorted by model distance: nonbonded pdb=" OG SER C 388 " pdb=" O6 NAG l 1 " model vdw 1.786 3.040 nonbonded pdb=" O ASN C 392 " pdb=" OD1 ASN C 392 " model vdw 1.902 3.040 nonbonded pdb=" NH2 ARG J 100A" pdb=" OE2 GLU J 100N" model vdw 2.035 3.120 nonbonded pdb=" OH TYR C 61 " pdb=" C HIS C 66 " model vdw 2.039 3.270 nonbonded pdb=" OE2 GLU L 70 " pdb=" N2 NAG 3 1 " model vdw 2.059 3.120 ... (remaining 185368 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 398 or resid 412 through 634)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 639)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 704)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'd' selection = chain 'l' selection = chain 'y' } ncs_group { reference = (chain 'T' and (resid 1 or resid 4 through 6)) selection = (chain 'U' and (resid 2 or resid 5 through 7)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 's' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Y' selection = chain 'k' selection = chain 'x' } ncs_group { reference = chain 'g' selection = chain 'q' selection = chain 't' } 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.480 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.015 0.202 23602 Z= 0.935 Angle : 2.142 41.455 32342 Z= 1.190 Chirality : 0.123 2.226 3977 Planarity : 0.013 0.112 3838 Dihedral : 14.727 101.676 10948 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.74 % Favored : 98.07 % Rotamer: Outliers : 0.39 % Allowed : 0.91 % Favored : 98.70 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 2.30 (0.17), residues: 2589 helix: -0.59 (0.22), residues: 419 sheet: 0.60 (0.16), residues: 830 loop : 3.32 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.046 0.006 TYR N 36 PHE 0.023 0.005 PHE I 78 TRP 0.058 0.009 TRP H 103 HIS 0.016 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01490 (23404) covalent geometry : angle 1.85220 (31789) SS BOND : bond 0.05934 ( 41) SS BOND : angle 2.95551 ( 82) hydrogen bonds : bond 0.19045 ( 816) hydrogen bonds : angle 8.20614 ( 2022) link_ALPHA1-2 : bond 0.02415 ( 6) link_ALPHA1-2 : angle 3.92137 ( 18) link_ALPHA1-3 : bond 0.03138 ( 16) link_ALPHA1-3 : angle 3.16967 ( 48) link_ALPHA1-6 : bond 0.02713 ( 14) link_ALPHA1-6 : angle 6.59770 ( 42) link_BETA1-4 : bond 0.03548 ( 58) link_BETA1-4 : angle 5.10700 ( 174) link_NAG-ASN : bond 0.03929 ( 63) link_NAG-ASN : angle 12.91374 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 829 time to evaluate : 0.853 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8893 (mt) cc_final: 0.8617 (mm) REVERT: A 96 TRP cc_start: 0.8585 (m-90) cc_final: 0.7417 (m-90) REVERT: A 100 MET cc_start: 0.8688 (mtp) cc_final: 0.8458 (ttp) REVERT: A 111 LEU cc_start: 0.9581 (mt) cc_final: 0.9195 (mt) REVERT: A 116 LEU cc_start: 0.9364 (tp) cc_final: 0.9120 (tt) REVERT: A 257 THR cc_start: 0.8540 (p) cc_final: 0.8257 (t) REVERT: A 359 ILE cc_start: 0.9194 (mt) cc_final: 0.8944 (mm) REVERT: A 434 MET cc_start: 0.8813 (ptm) cc_final: 0.8430 (ptm) REVERT: A 435 TYR cc_start: 0.8224 (t80) cc_final: 0.7848 (t80) REVERT: B 617 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7410 (mtp180) REVERT: B 621 GLU cc_start: 0.8687 (tt0) cc_final: 0.8423 (tt0) REVERT: B 623 TRP cc_start: 0.8035 (m100) cc_final: 0.7771 (m100) REVERT: B 630 GLN cc_start: 0.8664 (mt0) cc_final: 0.8201 (mp10) REVERT: B 634 GLU cc_start: 0.7964 (tt0) cc_final: 0.6753 (tp30) REVERT: B 658 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8774 (tm-30) REVERT: C 107 ASP cc_start: 0.8428 (t70) cc_final: 0.8219 (t70) REVERT: C 111 LEU cc_start: 0.9321 (mt) cc_final: 0.9050 (tt) REVERT: C 260 LEU cc_start: 0.9284 (mt) cc_final: 0.8987 (mp) REVERT: C 271 MET cc_start: 0.8266 (mmm) cc_final: 0.7748 (mmm) REVERT: C 308 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8719 (ttp80) REVERT: C 309 ILE cc_start: 0.9508 (mt) cc_final: 0.9301 (mt) REVERT: C 368 ASP cc_start: 0.8101 (m-30) cc_final: 0.7879 (m-30) REVERT: C 443 ILE cc_start: 0.8898 (mt) cc_final: 0.8277 (mm) REVERT: D 86 LEU cc_start: 0.9352 (mt) cc_final: 0.9146 (mp) REVERT: D 107 ASP cc_start: 0.8992 (t70) cc_final: 0.8712 (t0) REVERT: D 226 LEU cc_start: 0.8860 (mt) cc_final: 0.8634 (mt) REVERT: D 300 ASN cc_start: 0.8822 (m-40) cc_final: 0.7736 (m-40) REVERT: D 303 THR cc_start: 0.8702 (p) cc_final: 0.8184 (t) REVERT: D 368 ASP cc_start: 0.8647 (t70) cc_final: 0.8391 (t0) REVERT: D 370 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8234 (mt-10) REVERT: D 443 ILE cc_start: 0.9296 (mm) cc_final: 0.9039 (mm) REVERT: E 544 LEU cc_start: 0.9095 (mt) cc_final: 0.8844 (mt) REVERT: E 571 TRP cc_start: 0.6541 (m-10) cc_final: 0.5635 (m-10) REVERT: E 618 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7229 (m-40) REVERT: F 575 GLN cc_start: 0.8879 (tt0) cc_final: 0.8285 (tm-30) REVERT: F 601 LYS cc_start: 0.8596 (mppt) cc_final: 0.8120 (mtmm) REVERT: F 607 ASN cc_start: 0.7709 (t0) cc_final: 0.7420 (t0) REVERT: F 624 ASP cc_start: 0.8110 (m-30) cc_final: 0.7530 (p0) REVERT: G 36 TRP cc_start: 0.9046 (m100) cc_final: 0.8598 (m100) REVERT: G 100 PHE cc_start: 0.9415 (m-80) cc_final: 0.8726 (m-80) REVERT: H 23 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7046 (mm-30) REVERT: H 37 TRP cc_start: 0.9466 (m100) cc_final: 0.8661 (m-10) REVERT: H 56 GLN cc_start: 0.8127 (tp40) cc_final: 0.7722 (tp-100) REVERT: H 72 ASP cc_start: 0.8948 (p0) cc_final: 0.8074 (p0) REVERT: H 80 MET cc_start: 0.8756 (tmm) cc_final: 0.8308 (tmm) REVERT: H 86 ASP cc_start: 0.8442 (m-30) cc_final: 0.8066 (m-30) REVERT: H 99 TYR cc_start: 0.8197 (m-80) cc_final: 0.7962 (m-80) REVERT: H 100 ASP cc_start: 0.7968 (m-30) cc_final: 0.7722 (t0) REVERT: I 58 ASN cc_start: 0.8870 (t0) cc_final: 0.8596 (t0) REVERT: I 59 ASN cc_start: 0.9581 (m-40) cc_final: 0.8869 (m-40) REVERT: I 61 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8593 (tmm-80) REVERT: I 62 GLN cc_start: 0.9194 (tt0) cc_final: 0.8947 (tt0) REVERT: I 81 ASP cc_start: 0.8454 (m-30) cc_final: 0.8220 (m-30) REVERT: J 41 THR cc_start: 0.8646 (m) cc_final: 0.8333 (t) REVERT: J 80 MET cc_start: 0.6444 (ttp) cc_final: 0.6243 (ttt) REVERT: J 81 GLU cc_start: 0.6996 (tt0) cc_final: 0.6758 (tm-30) REVERT: K 5 THR cc_start: 0.8247 (p) cc_final: 0.7519 (p) REVERT: K 15 VAL cc_start: 0.8813 (t) cc_final: 0.8607 (m) REVERT: K 17 ASP cc_start: 0.8440 (m-30) cc_final: 0.8199 (m-30) REVERT: K 33 LEU cc_start: 0.8839 (tp) cc_final: 0.8630 (tp) REVERT: K 36 TYR cc_start: 0.8743 (m-80) cc_final: 0.7707 (m-80) REVERT: K 42 LYS cc_start: 0.8643 (mttt) cc_final: 0.8143 (tptp) REVERT: K 62 PHE cc_start: 0.7776 (m-80) cc_final: 0.7192 (m-80) REVERT: K 75 ILE cc_start: 0.8329 (mt) cc_final: 0.7879 (mt) REVERT: K 76 ASN cc_start: 0.8779 (m-40) cc_final: 0.8236 (p0) REVERT: K 82 ASP cc_start: 0.8338 (m-30) cc_final: 0.7908 (m-30) REVERT: L 46 LEU cc_start: 0.9176 (tp) cc_final: 0.8716 (tp) REVERT: L 97 PHE cc_start: 0.8545 (m-80) cc_final: 0.8248 (m-10) REVERT: M 34 ASN cc_start: 0.8756 (m-40) cc_final: 0.8063 (m110) REVERT: M 50 ASP cc_start: 0.8957 (t0) cc_final: 0.8573 (t0) REVERT: M 99 VAL cc_start: 0.9324 (p) cc_final: 0.8916 (p) REVERT: N 35 TRP cc_start: 0.4092 (m100) cc_final: 0.2709 (m100) REVERT: N 44 PRO cc_start: 0.7209 (Cg_exo) cc_final: 0.6461 (Cg_endo) REVERT: N 73 LEU cc_start: 0.7970 (tp) cc_final: 0.7212 (pp) REVERT: N 78 VAL cc_start: 0.5635 (t) cc_final: 0.5296 (t) REVERT: N 81 ASP cc_start: 0.8404 (m-30) cc_final: 0.7897 (m-30) outliers start: 9 outliers final: 3 residues processed: 838 average time/residue: 0.1743 time to fit residues: 216.5952 Evaluate side-chains 471 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 467 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 352 HIS A 356 ASN B 625 ASN C 66 HIS C 330 HIS C 352 HIS C 425 ASN D 315 GLN D 352 HIS G 64 GLN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 98 HIS L 24 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080249 restraints weight = 78359.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082282 restraints weight = 45122.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083656 restraints weight = 31286.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084551 restraints weight = 24441.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085149 restraints weight = 20751.075| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23602 Z= 0.244 Angle : 1.069 22.414 32342 Z= 0.490 Chirality : 0.055 0.637 3977 Planarity : 0.007 0.086 3838 Dihedral : 13.835 76.831 6038 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.45 (0.16), residues: 2589 helix: 0.60 (0.26), residues: 411 sheet: 0.37 (0.17), residues: 809 loop : 1.75 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 61 TYR 0.026 0.002 TYR E 638 PHE 0.044 0.003 PHE H 73 TRP 0.036 0.003 TRP I 37 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00533 (23404) covalent geometry : angle 0.91319 (31789) SS BOND : bond 0.00614 ( 41) SS BOND : angle 1.63454 ( 82) hydrogen bonds : bond 0.06151 ( 816) hydrogen bonds : angle 6.58637 ( 2022) link_ALPHA1-2 : bond 0.00267 ( 6) link_ALPHA1-2 : angle 1.87368 ( 18) link_ALPHA1-3 : bond 0.00760 ( 16) link_ALPHA1-3 : angle 2.30220 ( 48) link_ALPHA1-6 : bond 0.00679 ( 14) link_ALPHA1-6 : angle 2.29440 ( 42) link_BETA1-4 : bond 0.00515 ( 58) link_BETA1-4 : angle 2.92061 ( 174) link_NAG-ASN : bond 0.00843 ( 63) link_NAG-ASN : angle 6.58995 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 618 time to evaluate : 1.028 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8078 (t0) cc_final: 0.7821 (t0) REVERT: A 111 LEU cc_start: 0.9534 (mt) cc_final: 0.9137 (mt) REVERT: A 116 LEU cc_start: 0.9249 (tp) cc_final: 0.8927 (tt) REVERT: A 150 MET cc_start: 0.9002 (mmm) cc_final: 0.8376 (mtp) REVERT: A 180 ASP cc_start: 0.8049 (m-30) cc_final: 0.7775 (m-30) REVERT: A 257 THR cc_start: 0.8293 (p) cc_final: 0.7976 (t) REVERT: A 434 MET cc_start: 0.8501 (ptm) cc_final: 0.8280 (ptm) REVERT: A 435 TYR cc_start: 0.8210 (t80) cc_final: 0.7977 (t80) REVERT: B 530 MET cc_start: 0.8858 (mtp) cc_final: 0.8635 (mtt) REVERT: B 539 VAL cc_start: 0.9023 (t) cc_final: 0.8793 (t) REVERT: B 571 TRP cc_start: 0.7780 (m100) cc_final: 0.7215 (m100) REVERT: B 621 GLU cc_start: 0.8730 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 622 ILE cc_start: 0.8986 (mt) cc_final: 0.8752 (mm) REVERT: B 634 GLU cc_start: 0.8190 (tt0) cc_final: 0.7147 (tp30) REVERT: C 80 ASN cc_start: 0.8482 (t0) cc_final: 0.8104 (p0) REVERT: C 161 MET cc_start: 0.6606 (ttm) cc_final: 0.6204 (ttm) REVERT: C 201 ILE cc_start: 0.8861 (tt) cc_final: 0.8486 (tt) REVERT: C 211 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8223 (mm-30) REVERT: C 260 LEU cc_start: 0.9272 (mt) cc_final: 0.9066 (mp) REVERT: C 308 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8407 (mtp85) REVERT: C 309 ILE cc_start: 0.9097 (mt) cc_final: 0.8869 (mm) REVERT: C 345 VAL cc_start: 0.9365 (t) cc_final: 0.9111 (p) REVERT: C 426 MET cc_start: 0.8720 (tpt) cc_final: 0.8488 (ttm) REVERT: D 69 TRP cc_start: 0.8811 (m100) cc_final: 0.8604 (m100) REVERT: D 86 LEU cc_start: 0.9280 (mt) cc_final: 0.9071 (mp) REVERT: D 95 MET cc_start: 0.8045 (ttp) cc_final: 0.7697 (ttm) REVERT: D 279 ASN cc_start: 0.9132 (t0) cc_final: 0.8785 (t0) REVERT: D 300 ASN cc_start: 0.8499 (m-40) cc_final: 0.8293 (t0) REVERT: D 370 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7884 (mt-10) REVERT: E 530 MET cc_start: 0.9241 (mmm) cc_final: 0.8783 (mmm) REVERT: E 538 THR cc_start: 0.9430 (t) cc_final: 0.8099 (t) REVERT: E 571 TRP cc_start: 0.5816 (m-10) cc_final: 0.5278 (m-10) REVERT: E 610 TRP cc_start: 0.6652 (p-90) cc_final: 0.6339 (p-90) REVERT: E 626 MET cc_start: 0.8266 (ttt) cc_final: 0.7477 (ttt) REVERT: F 530 MET cc_start: 0.8735 (ptm) cc_final: 0.8497 (ptm) REVERT: F 584 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7987 (tm-30) REVERT: F 607 ASN cc_start: 0.7847 (t0) cc_final: 0.6959 (t0) REVERT: G 23 GLU cc_start: 0.8845 (pm20) cc_final: 0.8452 (mp0) REVERT: G 54 THR cc_start: 0.8487 (p) cc_final: 0.7713 (p) REVERT: G 96 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7525 (ttp80) REVERT: G 99 TYR cc_start: 0.8989 (m-80) cc_final: 0.8706 (m-80) REVERT: G 100 PHE cc_start: 0.9240 (m-80) cc_final: 0.8497 (m-80) REVERT: H 72 ASP cc_start: 0.8422 (p0) cc_final: 0.7934 (p0) REVERT: H 74 ASP cc_start: 0.7147 (p0) cc_final: 0.6861 (p0) REVERT: H 79 TYR cc_start: 0.8910 (m-80) cc_final: 0.8564 (m-10) REVERT: H 80 MET cc_start: 0.8482 (tmm) cc_final: 0.7977 (tmm) REVERT: H 86 ASP cc_start: 0.8624 (m-30) cc_final: 0.8292 (m-30) REVERT: H 103 TRP cc_start: 0.7442 (m-90) cc_final: 0.6915 (m-90) REVERT: I 23 GLU cc_start: 0.8244 (tt0) cc_final: 0.7778 (tp30) REVERT: I 58 ASN cc_start: 0.9051 (t0) cc_final: 0.8739 (t0) REVERT: I 59 ASN cc_start: 0.9152 (m-40) cc_final: 0.8828 (m110) REVERT: I 76 TYR cc_start: 0.7936 (m-80) cc_final: 0.7665 (m-10) REVERT: I 78 PHE cc_start: 0.9083 (m-10) cc_final: 0.8861 (m-10) REVERT: J 38 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7131 (ttp80) REVERT: J 41 THR cc_start: 0.8590 (m) cc_final: 0.8010 (t) REVERT: J 48 MET cc_start: 0.7655 (mmp) cc_final: 0.7174 (mmm) REVERT: J 61 PHE cc_start: 0.6660 (m-10) cc_final: 0.5995 (m-10) REVERT: K 5 THR cc_start: 0.7682 (p) cc_final: 0.7272 (p) REVERT: K 33 LEU cc_start: 0.8847 (tp) cc_final: 0.8475 (tp) REVERT: K 36 TYR cc_start: 0.8699 (m-80) cc_final: 0.7569 (m-10) REVERT: K 42 LYS cc_start: 0.8849 (mttt) cc_final: 0.8508 (mmtm) REVERT: K 49 TYR cc_start: 0.7141 (m-80) cc_final: 0.5991 (m-10) REVERT: K 54 LEU cc_start: 0.8625 (pp) cc_final: 0.8374 (pp) REVERT: K 58 VAL cc_start: 0.8038 (t) cc_final: 0.7625 (t) REVERT: K 76 ASN cc_start: 0.8600 (m-40) cc_final: 0.8309 (p0) REVERT: K 82 ASP cc_start: 0.8385 (m-30) cc_final: 0.8063 (m-30) REVERT: L 37 GLN cc_start: 0.8470 (pp30) cc_final: 0.8262 (pp30) REVERT: M 33 LEU cc_start: 0.9093 (tp) cc_final: 0.8890 (tp) REVERT: M 36 TYR cc_start: 0.8778 (m-80) cc_final: 0.8534 (m-80) REVERT: M 50 ASP cc_start: 0.8802 (t0) cc_final: 0.8374 (t0) REVERT: M 99 VAL cc_start: 0.9407 (p) cc_final: 0.9062 (p) REVERT: N 32 TYR cc_start: 0.6984 (m-80) cc_final: 0.6744 (m-80) REVERT: N 35 TRP cc_start: 0.6924 (m100) cc_final: 0.5996 (m100) REVERT: N 36 TYR cc_start: 0.7166 (m-80) cc_final: 0.6806 (m-10) REVERT: N 37 LEU cc_start: 0.8707 (tt) cc_final: 0.8242 (tp) REVERT: N 47 LEU cc_start: 0.8777 (mt) cc_final: 0.8420 (mp) REVERT: N 73 LEU cc_start: 0.8431 (tp) cc_final: 0.7892 (pt) outliers start: 1 outliers final: 1 residues processed: 619 average time/residue: 0.1587 time to fit residues: 152.4143 Evaluate side-chains 428 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 116 optimal weight: 0.8980 chunk 255 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN J 43 GLN K 26 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081823 restraints weight = 80052.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083887 restraints weight = 46305.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085264 restraints weight = 32004.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086169 restraints weight = 24920.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086699 restraints weight = 21076.584| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23602 Z= 0.153 Angle : 0.883 19.239 32342 Z= 0.405 Chirality : 0.049 0.436 3977 Planarity : 0.005 0.065 3838 Dihedral : 11.824 74.317 6038 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.14 (0.16), residues: 2589 helix: 0.88 (0.27), residues: 406 sheet: 0.22 (0.17), residues: 822 loop : 1.33 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 61 TYR 0.022 0.002 TYR C 217 PHE 0.033 0.002 PHE C 159 TRP 0.036 0.002 TRP A 96 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00320 (23404) covalent geometry : angle 0.75983 (31789) SS BOND : bond 0.00450 ( 41) SS BOND : angle 1.47041 ( 82) hydrogen bonds : bond 0.04956 ( 816) hydrogen bonds : angle 6.12378 ( 2022) link_ALPHA1-2 : bond 0.00332 ( 6) link_ALPHA1-2 : angle 1.82254 ( 18) link_ALPHA1-3 : bond 0.00948 ( 16) link_ALPHA1-3 : angle 1.87911 ( 48) link_ALPHA1-6 : bond 0.00874 ( 14) link_ALPHA1-6 : angle 2.15962 ( 42) link_BETA1-4 : bond 0.00425 ( 58) link_BETA1-4 : angle 2.57244 ( 174) link_NAG-ASN : bond 0.00522 ( 63) link_NAG-ASN : angle 5.20112 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 584 time to evaluate : 0.828 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9044 (m-90) cc_final: 0.8781 (m-90) REVERT: A 82 GLN cc_start: 0.8451 (pm20) cc_final: 0.7840 (pp30) REVERT: A 111 LEU cc_start: 0.9502 (mt) cc_final: 0.9048 (mt) REVERT: A 150 MET cc_start: 0.8887 (mmm) cc_final: 0.8440 (mtp) REVERT: A 180 ASP cc_start: 0.8106 (m-30) cc_final: 0.7853 (m-30) REVERT: A 377 ASN cc_start: 0.8976 (t0) cc_final: 0.8753 (t0) REVERT: B 530 MET cc_start: 0.8770 (mtp) cc_final: 0.8518 (mtt) REVERT: B 571 TRP cc_start: 0.7776 (m100) cc_final: 0.7173 (m100) REVERT: B 634 GLU cc_start: 0.7876 (tt0) cc_final: 0.6865 (tp30) REVERT: B 635 ILE cc_start: 0.8524 (pt) cc_final: 0.7573 (pt) REVERT: C 80 ASN cc_start: 0.8655 (t0) cc_final: 0.8215 (p0) REVERT: C 110 SER cc_start: 0.9130 (m) cc_final: 0.8693 (p) REVERT: C 161 MET cc_start: 0.6838 (ttm) cc_final: 0.6544 (ttm) REVERT: C 195 ASN cc_start: 0.9014 (p0) cc_final: 0.8736 (p0) REVERT: C 201 ILE cc_start: 0.8899 (tt) cc_final: 0.8518 (tt) REVERT: C 308 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8341 (mtp85) REVERT: C 309 ILE cc_start: 0.9094 (mt) cc_final: 0.8832 (tt) REVERT: D 42 VAL cc_start: 0.9348 (m) cc_final: 0.9145 (p) REVERT: D 69 TRP cc_start: 0.8716 (m100) cc_final: 0.8407 (m100) REVERT: D 95 MET cc_start: 0.7985 (ttp) cc_final: 0.7602 (ttm) REVERT: D 365 SER cc_start: 0.8435 (m) cc_final: 0.7859 (t) REVERT: E 536 THR cc_start: 0.8685 (p) cc_final: 0.8176 (p) REVERT: E 538 THR cc_start: 0.9071 (t) cc_final: 0.8517 (t) REVERT: E 571 TRP cc_start: 0.5736 (m-10) cc_final: 0.5053 (m-10) REVERT: F 575 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6713 (tm-30) REVERT: F 579 ARG cc_start: 0.8373 (mtm180) cc_final: 0.7998 (mtt180) REVERT: F 584 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8181 (tm-30) REVERT: F 624 ASP cc_start: 0.7645 (m-30) cc_final: 0.7407 (m-30) REVERT: G 31 ASP cc_start: 0.8415 (p0) cc_final: 0.8113 (p0) REVERT: G 54 THR cc_start: 0.8516 (p) cc_final: 0.7811 (p) REVERT: G 91 PHE cc_start: 0.7819 (p90) cc_final: 0.7344 (p90) REVERT: G 95 GLN cc_start: 0.9237 (tt0) cc_final: 0.8740 (tt0) REVERT: G 100 PHE cc_start: 0.9135 (m-80) cc_final: 0.8587 (m-80) REVERT: H 30 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8053 (mtt-85) REVERT: H 72 ASP cc_start: 0.8500 (p0) cc_final: 0.7914 (p0) REVERT: H 74 ASP cc_start: 0.7183 (p0) cc_final: 0.6962 (p0) REVERT: H 79 TYR cc_start: 0.8887 (m-80) cc_final: 0.8563 (m-10) REVERT: H 80 MET cc_start: 0.8698 (tmm) cc_final: 0.8135 (tmm) REVERT: I 28 ASN cc_start: 0.8225 (t0) cc_final: 0.7637 (t0) REVERT: I 58 ASN cc_start: 0.8996 (t0) cc_final: 0.8749 (t0) REVERT: I 59 ASN cc_start: 0.8962 (m-40) cc_final: 0.8436 (m110) REVERT: J 41 THR cc_start: 0.8551 (m) cc_final: 0.8193 (t) REVERT: J 47 TRP cc_start: 0.8514 (t60) cc_final: 0.6861 (t60) REVERT: J 48 MET cc_start: 0.7800 (mmp) cc_final: 0.7017 (mmm) REVERT: J 108 TRP cc_start: 0.7840 (m-10) cc_final: 0.6977 (m-10) REVERT: K 33 LEU cc_start: 0.8565 (tp) cc_final: 0.8326 (tp) REVERT: K 36 TYR cc_start: 0.8521 (m-80) cc_final: 0.7879 (m-10) REVERT: K 37 GLN cc_start: 0.8619 (pp30) cc_final: 0.8402 (pp30) REVERT: K 42 LYS cc_start: 0.8951 (mttt) cc_final: 0.8680 (mmtm) REVERT: K 46 LEU cc_start: 0.8994 (tp) cc_final: 0.8577 (tp) REVERT: K 54 LEU cc_start: 0.8984 (pp) cc_final: 0.8415 (pp) REVERT: K 75 ILE cc_start: 0.8734 (mm) cc_final: 0.8402 (mm) REVERT: K 82 ASP cc_start: 0.8310 (m-30) cc_final: 0.8061 (m-30) REVERT: L 1 ASP cc_start: 0.6946 (m-30) cc_final: 0.6739 (m-30) REVERT: L 37 GLN cc_start: 0.8521 (pp30) cc_final: 0.8083 (pp30) REVERT: L 46 LEU cc_start: 0.9119 (tp) cc_final: 0.8902 (tt) REVERT: M 34 ASN cc_start: 0.9031 (m-40) cc_final: 0.8255 (m-40) REVERT: M 50 ASP cc_start: 0.8465 (t0) cc_final: 0.7921 (t0) REVERT: M 99 VAL cc_start: 0.9354 (p) cc_final: 0.9085 (p) REVERT: N 37 LEU cc_start: 0.8710 (tt) cc_final: 0.8344 (tp) REVERT: N 44 PRO cc_start: 0.9081 (Cg_exo) cc_final: 0.8536 (Cg_endo) outliers start: 2 outliers final: 1 residues processed: 585 average time/residue: 0.1556 time to fit residues: 139.9734 Evaluate side-chains 420 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 234 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN E 591 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 1 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080418 restraints weight = 80064.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082366 restraints weight = 47154.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083674 restraints weight = 33181.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084454 restraints weight = 26230.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085054 restraints weight = 22570.603| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23602 Z= 0.155 Angle : 0.835 17.965 32342 Z= 0.381 Chirality : 0.048 0.477 3977 Planarity : 0.005 0.062 3838 Dihedral : 10.472 64.869 6038 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.02 (0.16), residues: 2589 helix: 1.01 (0.27), residues: 402 sheet: 0.23 (0.17), residues: 816 loop : 1.08 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 61 TYR 0.018 0.001 TYR E 638 PHE 0.030 0.002 PHE H 91 TRP 0.032 0.002 TRP J 108 HIS 0.010 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00338 (23404) covalent geometry : angle 0.72917 (31789) SS BOND : bond 0.00460 ( 41) SS BOND : angle 1.29225 ( 82) hydrogen bonds : bond 0.04437 ( 816) hydrogen bonds : angle 5.95372 ( 2022) link_ALPHA1-2 : bond 0.00449 ( 6) link_ALPHA1-2 : angle 1.75353 ( 18) link_ALPHA1-3 : bond 0.00967 ( 16) link_ALPHA1-3 : angle 1.87381 ( 48) link_ALPHA1-6 : bond 0.00840 ( 14) link_ALPHA1-6 : angle 2.04302 ( 42) link_BETA1-4 : bond 0.00374 ( 58) link_BETA1-4 : angle 2.39891 ( 174) link_NAG-ASN : bond 0.00419 ( 63) link_NAG-ASN : angle 4.65725 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 538 time to evaluate : 0.771 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9038 (m-90) cc_final: 0.8792 (m-90) REVERT: A 111 LEU cc_start: 0.9449 (mt) cc_final: 0.9030 (mt) REVERT: A 150 MET cc_start: 0.8827 (mmm) cc_final: 0.8525 (mtp) REVERT: A 426 MET cc_start: 0.8696 (tpt) cc_final: 0.8494 (tpp) REVERT: A 427 TRP cc_start: 0.8678 (m-90) cc_final: 0.8140 (m-90) REVERT: B 571 TRP cc_start: 0.7708 (m100) cc_final: 0.7286 (m100) REVERT: B 622 ILE cc_start: 0.8749 (mm) cc_final: 0.8503 (mm) REVERT: B 634 GLU cc_start: 0.7860 (tt0) cc_final: 0.7128 (tp30) REVERT: C 80 ASN cc_start: 0.8787 (t0) cc_final: 0.8541 (p0) REVERT: C 161 MET cc_start: 0.6635 (ttm) cc_final: 0.6372 (ttm) REVERT: C 195 ASN cc_start: 0.8961 (p0) cc_final: 0.8596 (p0) REVERT: C 201 ILE cc_start: 0.8845 (tt) cc_final: 0.8467 (tt) REVERT: C 260 LEU cc_start: 0.9177 (mt) cc_final: 0.8945 (mp) REVERT: C 308 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8380 (mtp85) REVERT: C 309 ILE cc_start: 0.9038 (mt) cc_final: 0.8787 (tt) REVERT: C 427 TRP cc_start: 0.8820 (m-90) cc_final: 0.8273 (m-10) REVERT: D 69 TRP cc_start: 0.8647 (m100) cc_final: 0.8350 (m100) REVERT: D 95 MET cc_start: 0.7993 (ttp) cc_final: 0.7569 (ttm) REVERT: E 536 THR cc_start: 0.8593 (p) cc_final: 0.8350 (p) REVERT: E 581 LEU cc_start: 0.9316 (tp) cc_final: 0.9087 (tp) REVERT: E 626 MET cc_start: 0.7817 (ttt) cc_final: 0.7362 (ttt) REVERT: F 579 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8235 (mtm180) REVERT: F 584 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 54 THR cc_start: 0.8083 (p) cc_final: 0.7858 (p) REVERT: G 80 MET cc_start: 0.8127 (ptm) cc_final: 0.7848 (ptm) REVERT: G 91 PHE cc_start: 0.8229 (p90) cc_final: 0.7863 (p90) REVERT: G 96 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7737 (ttp80) REVERT: G 100 ASP cc_start: 0.8051 (t70) cc_final: 0.7689 (t0) REVERT: G 100 PHE cc_start: 0.9025 (m-80) cc_final: 0.8067 (m-80) REVERT: H 28 ASN cc_start: 0.8006 (t0) cc_final: 0.7458 (t0) REVERT: H 72 ASP cc_start: 0.8559 (p0) cc_final: 0.7889 (p0) REVERT: H 80 MET cc_start: 0.8917 (tmm) cc_final: 0.8310 (tmm) REVERT: H 86 ASP cc_start: 0.8448 (m-30) cc_final: 0.8148 (m-30) REVERT: J 38 ARG cc_start: 0.7615 (ttp80) cc_final: 0.6992 (ttp80) REVERT: J 41 THR cc_start: 0.8565 (m) cc_final: 0.8207 (t) REVERT: J 48 MET cc_start: 0.7698 (mmp) cc_final: 0.7201 (mmm) REVERT: J 100 TYR cc_start: 0.8186 (t80) cc_final: 0.7746 (t80) REVERT: K 36 TYR cc_start: 0.8764 (m-80) cc_final: 0.7711 (m-10) REVERT: K 42 LYS cc_start: 0.8986 (mttt) cc_final: 0.8696 (mmtm) REVERT: K 54 LEU cc_start: 0.9002 (pp) cc_final: 0.8534 (pp) REVERT: K 75 ILE cc_start: 0.8749 (mm) cc_final: 0.8485 (mm) REVERT: K 82 ASP cc_start: 0.8196 (m-30) cc_final: 0.7353 (m-30) REVERT: L 37 GLN cc_start: 0.8549 (pp30) cc_final: 0.8227 (pp30) REVERT: L 97 PHE cc_start: 0.8706 (m-80) cc_final: 0.8391 (m-80) REVERT: M 34 ASN cc_start: 0.8908 (m-40) cc_final: 0.8691 (m-40) REVERT: M 50 ASP cc_start: 0.8411 (t0) cc_final: 0.7893 (t0) REVERT: M 99 VAL cc_start: 0.9309 (p) cc_final: 0.9097 (p) REVERT: N 8 PRO cc_start: 0.6797 (Cg_exo) cc_final: 0.6572 (Cg_endo) REVERT: N 27 HIS cc_start: 0.8255 (m90) cc_final: 0.8008 (m-70) REVERT: N 35 TRP cc_start: 0.6272 (m100) cc_final: 0.5935 (m100) REVERT: N 37 LEU cc_start: 0.8864 (tt) cc_final: 0.8605 (tp) REVERT: N 47 LEU cc_start: 0.8691 (mp) cc_final: 0.8447 (mp) REVERT: N 78 VAL cc_start: 0.6835 (t) cc_final: 0.6561 (t) outliers start: 2 outliers final: 1 residues processed: 540 average time/residue: 0.1534 time to fit residues: 127.8146 Evaluate side-chains 409 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 138 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN H 56 GLN K 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079105 restraints weight = 75900.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081170 restraints weight = 43007.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082570 restraints weight = 29423.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083427 restraints weight = 22723.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084071 restraints weight = 19209.968| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23602 Z= 0.138 Angle : 0.794 16.951 32342 Z= 0.366 Chirality : 0.048 0.630 3977 Planarity : 0.004 0.045 3838 Dihedral : 9.612 62.590 6038 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.93 (0.17), residues: 2589 helix: 1.06 (0.27), residues: 408 sheet: 0.19 (0.17), residues: 839 loop : 0.99 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 61 TYR 0.027 0.002 TYR H 99 PHE 0.026 0.002 PHE A 53 TRP 0.032 0.002 TRP A 45 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00296 (23404) covalent geometry : angle 0.69613 (31789) SS BOND : bond 0.00574 ( 41) SS BOND : angle 1.45954 ( 82) hydrogen bonds : bond 0.04159 ( 816) hydrogen bonds : angle 5.74358 ( 2022) link_ALPHA1-2 : bond 0.00381 ( 6) link_ALPHA1-2 : angle 1.73804 ( 18) link_ALPHA1-3 : bond 0.00995 ( 16) link_ALPHA1-3 : angle 1.83674 ( 48) link_ALPHA1-6 : bond 0.00824 ( 14) link_ALPHA1-6 : angle 1.97693 ( 42) link_BETA1-4 : bond 0.00416 ( 58) link_BETA1-4 : angle 2.23347 ( 174) link_NAG-ASN : bond 0.00498 ( 63) link_NAG-ASN : angle 4.35301 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9104 (m-90) cc_final: 0.8754 (m-90) REVERT: A 111 LEU cc_start: 0.9413 (mt) cc_final: 0.8981 (mt) REVERT: A 150 MET cc_start: 0.8862 (mmm) cc_final: 0.8396 (mmm) REVERT: A 426 MET cc_start: 0.8753 (tpt) cc_final: 0.8539 (tpp) REVERT: A 427 TRP cc_start: 0.8700 (m-90) cc_final: 0.8123 (m-90) REVERT: B 571 TRP cc_start: 0.7718 (m100) cc_final: 0.7284 (m100) REVERT: B 574 LYS cc_start: 0.9303 (mmtp) cc_final: 0.8823 (mttp) REVERT: B 634 GLU cc_start: 0.7749 (tt0) cc_final: 0.7395 (tp30) REVERT: B 648 GLU cc_start: 0.7207 (tp30) cc_final: 0.6990 (tp30) REVERT: C 80 ASN cc_start: 0.8835 (t0) cc_final: 0.8560 (p0) REVERT: C 161 MET cc_start: 0.6779 (ttm) cc_final: 0.6523 (ttm) REVERT: C 308 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8463 (mtp180) REVERT: C 309 ILE cc_start: 0.9086 (mt) cc_final: 0.8791 (tt) REVERT: C 345 VAL cc_start: 0.9371 (t) cc_final: 0.9169 (p) REVERT: C 426 MET cc_start: 0.8359 (ttm) cc_final: 0.8149 (ttm) REVERT: C 427 TRP cc_start: 0.8828 (m-90) cc_final: 0.8180 (m-10) REVERT: D 69 TRP cc_start: 0.8592 (m100) cc_final: 0.8378 (m100) REVERT: D 95 MET cc_start: 0.8039 (ttp) cc_final: 0.7590 (ttm) REVERT: D 365 SER cc_start: 0.8738 (m) cc_final: 0.8002 (t) REVERT: E 536 THR cc_start: 0.8552 (p) cc_final: 0.8279 (p) REVERT: E 542 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7870 (ttp-110) REVERT: E 626 MET cc_start: 0.8239 (ttt) cc_final: 0.7722 (ttt) REVERT: F 579 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8217 (mtm180) REVERT: F 584 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8316 (tm-30) REVERT: F 624 ASP cc_start: 0.7748 (m-30) cc_final: 0.7457 (m-30) REVERT: F 647 GLU cc_start: 0.7882 (tt0) cc_final: 0.7516 (tt0) REVERT: G 23 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7951 (mm-30) REVERT: G 91 PHE cc_start: 0.8247 (p90) cc_final: 0.7775 (p90) REVERT: G 95 GLN cc_start: 0.9129 (tt0) cc_final: 0.8761 (tt0) REVERT: G 98 ASP cc_start: 0.8975 (m-30) cc_final: 0.8728 (m-30) REVERT: G 100 ASP cc_start: 0.7829 (t70) cc_final: 0.7453 (t0) REVERT: G 100 PHE cc_start: 0.8984 (m-80) cc_final: 0.8250 (m-80) REVERT: H 28 ASN cc_start: 0.8003 (t0) cc_final: 0.7388 (t0) REVERT: H 80 MET cc_start: 0.9035 (tmm) cc_final: 0.8315 (tmm) REVERT: H 86 ASP cc_start: 0.8357 (m-30) cc_final: 0.8057 (m-30) REVERT: I 28 ASN cc_start: 0.7924 (t0) cc_final: 0.7666 (t0) REVERT: I 70 THR cc_start: 0.8730 (m) cc_final: 0.8407 (t) REVERT: J 38 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7092 (ttp80) REVERT: J 41 THR cc_start: 0.8524 (m) cc_final: 0.7987 (t) REVERT: J 47 TRP cc_start: 0.8505 (t60) cc_final: 0.7981 (t60) REVERT: J 48 MET cc_start: 0.7648 (mmp) cc_final: 0.7016 (mmm) REVERT: J 80 MET cc_start: 0.7122 (ttt) cc_final: 0.6904 (ttt) REVERT: J 100 TYR cc_start: 0.8361 (t80) cc_final: 0.8059 (t80) REVERT: J 105 LEU cc_start: 0.8841 (mt) cc_final: 0.8631 (mt) REVERT: J 108 TRP cc_start: 0.7484 (m-10) cc_final: 0.7273 (m-10) REVERT: K 3 GLN cc_start: 0.7273 (mp10) cc_final: 0.7016 (mp10) REVERT: K 36 TYR cc_start: 0.8843 (m-80) cc_final: 0.8342 (m-10) REVERT: K 42 LYS cc_start: 0.8971 (mttt) cc_final: 0.8678 (mmtm) REVERT: K 54 LEU cc_start: 0.9023 (pp) cc_final: 0.8566 (pp) REVERT: K 75 ILE cc_start: 0.8838 (mm) cc_final: 0.8534 (mm) REVERT: K 82 ASP cc_start: 0.8116 (m-30) cc_final: 0.7561 (m-30) REVERT: L 97 PHE cc_start: 0.8732 (m-80) cc_final: 0.8305 (m-80) REVERT: M 34 ASN cc_start: 0.8867 (m-40) cc_final: 0.8662 (m-40) REVERT: M 50 ASP cc_start: 0.8293 (t0) cc_final: 0.7807 (t0) REVERT: M 69 GLN cc_start: 0.7495 (pm20) cc_final: 0.6817 (mp10) REVERT: N 8 PRO cc_start: 0.6808 (Cg_exo) cc_final: 0.6603 (Cg_endo) REVERT: N 35 TRP cc_start: 0.6197 (m100) cc_final: 0.5848 (m100) REVERT: N 37 LEU cc_start: 0.9035 (tt) cc_final: 0.8659 (pt) REVERT: N 44 PRO cc_start: 0.9356 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: N 47 LEU cc_start: 0.8496 (mp) cc_final: 0.7838 (mp) REVERT: N 86 TYR cc_start: 0.7009 (m-80) cc_final: 0.6699 (m-10) outliers start: 1 outliers final: 0 residues processed: 531 average time/residue: 0.1548 time to fit residues: 127.1752 Evaluate side-chains 415 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 178 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 328 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN E 651 ASN ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 108 GLN I 1 GLN J 43 GLN ** J 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.074232 restraints weight = 78581.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076192 restraints weight = 44827.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077501 restraints weight = 30855.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078375 restraints weight = 24069.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078948 restraints weight = 20382.250| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23602 Z= 0.266 Angle : 0.904 17.166 32342 Z= 0.418 Chirality : 0.050 0.519 3977 Planarity : 0.005 0.051 3838 Dihedral : 9.610 62.677 6038 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.51 (0.16), residues: 2589 helix: 0.74 (0.26), residues: 411 sheet: -0.05 (0.17), residues: 798 loop : 0.66 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 542 TYR 0.023 0.002 TYR M 91 PHE 0.030 0.003 PHE A 53 TRP 0.029 0.003 TRP F 571 HIS 0.011 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00586 (23404) covalent geometry : angle 0.80929 (31789) SS BOND : bond 0.00517 ( 41) SS BOND : angle 1.47293 ( 82) hydrogen bonds : bond 0.04809 ( 816) hydrogen bonds : angle 5.87907 ( 2022) link_ALPHA1-2 : bond 0.00345 ( 6) link_ALPHA1-2 : angle 1.85571 ( 18) link_ALPHA1-3 : bond 0.00883 ( 16) link_ALPHA1-3 : angle 1.98872 ( 48) link_ALPHA1-6 : bond 0.00781 ( 14) link_ALPHA1-6 : angle 2.04208 ( 42) link_BETA1-4 : bond 0.00492 ( 58) link_BETA1-4 : angle 2.46859 ( 174) link_NAG-ASN : bond 0.00743 ( 63) link_NAG-ASN : angle 4.58283 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9109 (m-90) cc_final: 0.8756 (m-90) REVERT: A 111 LEU cc_start: 0.9450 (mt) cc_final: 0.9098 (mt) REVERT: A 150 MET cc_start: 0.8858 (mmm) cc_final: 0.8628 (mtp) REVERT: A 426 MET cc_start: 0.8743 (tpt) cc_final: 0.8491 (tpp) REVERT: B 571 TRP cc_start: 0.7853 (m100) cc_final: 0.7315 (m100) REVERT: B 634 GLU cc_start: 0.7959 (tt0) cc_final: 0.7616 (tp30) REVERT: C 150 MET cc_start: 0.9131 (mmm) cc_final: 0.8631 (mpp) REVERT: C 161 MET cc_start: 0.7355 (ttm) cc_final: 0.6702 (ttm) REVERT: C 309 ILE cc_start: 0.9045 (mt) cc_final: 0.8797 (mm) REVERT: D 95 MET cc_start: 0.8271 (ttp) cc_final: 0.7858 (ttm) REVERT: D 300 ASN cc_start: 0.8268 (t0) cc_final: 0.7771 (t0) REVERT: D 368 ASP cc_start: 0.8058 (t0) cc_final: 0.7845 (t0) REVERT: E 536 THR cc_start: 0.8652 (p) cc_final: 0.8386 (p) REVERT: E 581 LEU cc_start: 0.9400 (tp) cc_final: 0.9169 (tt) REVERT: F 530 MET cc_start: 0.8464 (ptm) cc_final: 0.8205 (ttp) REVERT: F 579 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8280 (mtm180) REVERT: F 584 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 624 ASP cc_start: 0.8026 (m-30) cc_final: 0.7670 (m-30) REVERT: G 54 THR cc_start: 0.8615 (p) cc_final: 0.8369 (p) REVERT: G 91 PHE cc_start: 0.8429 (p90) cc_final: 0.8101 (p90) REVERT: G 96 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8124 (ttp80) REVERT: G 98 ASP cc_start: 0.9027 (m-30) cc_final: 0.8815 (m-30) REVERT: G 100 PHE cc_start: 0.9132 (m-80) cc_final: 0.8518 (m-80) REVERT: H 28 ASN cc_start: 0.8062 (t0) cc_final: 0.7601 (t0) REVERT: H 80 MET cc_start: 0.9165 (tmm) cc_final: 0.8317 (tmm) REVERT: I 23 GLU cc_start: 0.8053 (tp30) cc_final: 0.7566 (tp30) REVERT: I 27 TYR cc_start: 0.9157 (p90) cc_final: 0.8954 (p90) REVERT: J 38 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7375 (ttp80) REVERT: J 41 THR cc_start: 0.8842 (m) cc_final: 0.8210 (t) REVERT: J 43 GLN cc_start: 0.8292 (mp10) cc_final: 0.8063 (mm-40) REVERT: J 47 TRP cc_start: 0.8213 (t60) cc_final: 0.7903 (t60) REVERT: J 48 MET cc_start: 0.7633 (mmp) cc_final: 0.6979 (mmm) REVERT: J 100 TYR cc_start: 0.8398 (t80) cc_final: 0.7400 (t80) REVERT: K 26 ASN cc_start: 0.7645 (m110) cc_final: 0.7254 (t0) REVERT: K 36 TYR cc_start: 0.8993 (m-80) cc_final: 0.7730 (m-10) REVERT: K 42 LYS cc_start: 0.9119 (mttt) cc_final: 0.8817 (mmtm) REVERT: K 54 LEU cc_start: 0.9065 (pp) cc_final: 0.8611 (pp) REVERT: K 65 ARG cc_start: 0.6494 (mtm110) cc_final: 0.6263 (mtm110) REVERT: K 75 ILE cc_start: 0.8850 (mm) cc_final: 0.8509 (mm) REVERT: L 37 GLN cc_start: 0.8622 (pp30) cc_final: 0.8287 (pp30) REVERT: L 97 PHE cc_start: 0.8843 (m-80) cc_final: 0.8391 (m-80) REVERT: M 50 ASP cc_start: 0.8477 (t0) cc_final: 0.8136 (t0) REVERT: M 69 GLN cc_start: 0.7696 (pm20) cc_final: 0.7077 (mp10) REVERT: N 8 PRO cc_start: 0.6729 (Cg_exo) cc_final: 0.6505 (Cg_endo) REVERT: N 37 LEU cc_start: 0.9104 (tt) cc_final: 0.8668 (pt) REVERT: N 47 LEU cc_start: 0.8701 (mp) cc_final: 0.8135 (mp) REVERT: N 78 VAL cc_start: 0.6725 (t) cc_final: 0.6407 (t) outliers start: 1 outliers final: 0 residues processed: 494 average time/residue: 0.1578 time to fit residues: 121.5924 Evaluate side-chains 378 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 3 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076267 restraints weight = 76814.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078343 restraints weight = 42851.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079737 restraints weight = 28837.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080664 restraints weight = 22167.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081214 restraints weight = 18531.434| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23602 Z= 0.151 Angle : 0.800 16.120 32342 Z= 0.370 Chirality : 0.048 0.470 3977 Planarity : 0.004 0.085 3838 Dihedral : 9.038 59.608 6038 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2589 helix: 0.89 (0.27), residues: 408 sheet: -0.00 (0.17), residues: 849 loop : 0.68 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 82A TYR 0.032 0.002 TYR H 99 PHE 0.022 0.002 PHE A 53 TRP 0.030 0.002 TRP A 45 HIS 0.005 0.001 HIS J 98 Details of bonding type rmsd covalent geometry : bond 0.00334 (23404) covalent geometry : angle 0.70751 (31789) SS BOND : bond 0.00440 ( 41) SS BOND : angle 1.22382 ( 82) hydrogen bonds : bond 0.04291 ( 816) hydrogen bonds : angle 5.68928 ( 2022) link_ALPHA1-2 : bond 0.00299 ( 6) link_ALPHA1-2 : angle 1.81770 ( 18) link_ALPHA1-3 : bond 0.00965 ( 16) link_ALPHA1-3 : angle 1.79054 ( 48) link_ALPHA1-6 : bond 0.00761 ( 14) link_ALPHA1-6 : angle 1.91732 ( 42) link_BETA1-4 : bond 0.00367 ( 58) link_BETA1-4 : angle 2.23261 ( 174) link_NAG-ASN : bond 0.00441 ( 63) link_NAG-ASN : angle 4.26641 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 0.831 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: A 69 TRP cc_start: 0.9074 (m-90) cc_final: 0.8596 (m-90) REVERT: A 111 LEU cc_start: 0.9420 (mt) cc_final: 0.9084 (mt) REVERT: A 150 MET cc_start: 0.8843 (mmm) cc_final: 0.8602 (mtp) REVERT: A 377 ASN cc_start: 0.9075 (t0) cc_final: 0.8869 (t0) REVERT: B 634 GLU cc_start: 0.8107 (tt0) cc_final: 0.7583 (tp30) REVERT: B 635 ILE cc_start: 0.8883 (pt) cc_final: 0.8050 (pt) REVERT: C 150 MET cc_start: 0.9094 (mmm) cc_final: 0.8515 (mpp) REVERT: C 308 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8367 (mtp180) REVERT: C 309 ILE cc_start: 0.9061 (mt) cc_final: 0.8610 (tt) REVERT: D 86 LEU cc_start: 0.9210 (mp) cc_final: 0.9001 (mp) REVERT: D 95 MET cc_start: 0.8071 (ttp) cc_final: 0.7763 (ttm) REVERT: D 125 LEU cc_start: 0.9368 (mt) cc_final: 0.9166 (mt) REVERT: D 300 ASN cc_start: 0.8275 (t0) cc_final: 0.7758 (t0) REVERT: D 492 GLU cc_start: 0.8167 (tt0) cc_final: 0.7572 (tm-30) REVERT: E 536 THR cc_start: 0.8591 (p) cc_final: 0.8323 (p) REVERT: F 530 MET cc_start: 0.8463 (ptm) cc_final: 0.8067 (ptm) REVERT: F 579 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8242 (mtm180) REVERT: F 584 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8450 (tm-30) REVERT: F 624 ASP cc_start: 0.7956 (m-30) cc_final: 0.7649 (m-30) REVERT: F 647 GLU cc_start: 0.7802 (tt0) cc_final: 0.7586 (tt0) REVERT: G 54 THR cc_start: 0.8412 (p) cc_final: 0.8167 (p) REVERT: G 72 ASP cc_start: 0.8002 (p0) cc_final: 0.7251 (p0) REVERT: G 98 ASP cc_start: 0.8972 (m-30) cc_final: 0.8749 (m-30) REVERT: H 28 ASN cc_start: 0.8086 (t0) cc_final: 0.7542 (t0) REVERT: H 72 ASP cc_start: 0.8595 (p0) cc_final: 0.8175 (p0) REVERT: H 79 TYR cc_start: 0.8791 (m-80) cc_final: 0.8276 (m-10) REVERT: H 80 MET cc_start: 0.9172 (tmm) cc_final: 0.8309 (tmm) REVERT: I 23 GLU cc_start: 0.7900 (tp30) cc_final: 0.7415 (tp30) REVERT: I 27 TYR cc_start: 0.9046 (p90) cc_final: 0.8829 (p90) REVERT: I 32 TYR cc_start: 0.8821 (m-10) cc_final: 0.8466 (m-10) REVERT: I 100 ASP cc_start: 0.8360 (m-30) cc_final: 0.7918 (p0) REVERT: J 41 THR cc_start: 0.8792 (m) cc_final: 0.8158 (t) REVERT: J 48 MET cc_start: 0.7693 (mmp) cc_final: 0.7105 (mmm) REVERT: J 80 MET cc_start: 0.6986 (ttt) cc_final: 0.6712 (ttp) REVERT: J 100 ARG cc_start: 0.9014 (ptm160) cc_final: 0.8628 (ptm160) REVERT: J 100 TYR cc_start: 0.8335 (t80) cc_final: 0.7949 (t80) REVERT: J 100 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8315 (mm-30) REVERT: J 100 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8812 (mt-10) REVERT: K 5 THR cc_start: 0.7813 (p) cc_final: 0.7445 (p) REVERT: K 36 TYR cc_start: 0.8836 (m-80) cc_final: 0.8132 (m-10) REVERT: K 42 LYS cc_start: 0.9093 (mttt) cc_final: 0.8790 (mmtm) REVERT: K 58 VAL cc_start: 0.8061 (t) cc_final: 0.7484 (t) REVERT: K 65 ARG cc_start: 0.6603 (mtm110) cc_final: 0.6347 (mtm110) REVERT: K 75 ILE cc_start: 0.8871 (mm) cc_final: 0.8554 (mm) REVERT: L 45 LYS cc_start: 0.8779 (tttt) cc_final: 0.8474 (ttpp) REVERT: L 97 PHE cc_start: 0.8784 (m-80) cc_final: 0.8392 (m-80) REVERT: M 50 ASP cc_start: 0.8434 (t0) cc_final: 0.7954 (t0) REVERT: M 69 GLN cc_start: 0.7803 (pm20) cc_final: 0.7351 (mp10) REVERT: N 36 TYR cc_start: 0.6763 (m-10) cc_final: 0.6255 (m-10) REVERT: N 37 LEU cc_start: 0.8975 (tt) cc_final: 0.8622 (pt) REVERT: N 47 LEU cc_start: 0.8612 (mp) cc_final: 0.8092 (mp) REVERT: N 79 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7292 (tm-30) outliers start: 2 outliers final: 0 residues processed: 507 average time/residue: 0.1594 time to fit residues: 125.5044 Evaluate side-chains 408 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 156 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 199 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 43 GLN K 26 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.092819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075576 restraints weight = 77649.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077568 restraints weight = 43932.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078907 restraints weight = 30054.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079803 restraints weight = 23227.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080308 restraints weight = 19480.794| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23602 Z= 0.186 Angle : 0.810 15.872 32342 Z= 0.378 Chirality : 0.048 0.408 3977 Planarity : 0.004 0.074 3838 Dihedral : 8.882 59.533 6038 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2589 helix: 0.91 (0.27), residues: 408 sheet: -0.17 (0.17), residues: 848 loop : 0.48 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG N 54 TYR 0.021 0.002 TYR N 36 PHE 0.023 0.002 PHE G 100B TRP 0.049 0.002 TRP J 108 HIS 0.010 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00416 (23404) covalent geometry : angle 0.72623 (31789) SS BOND : bond 0.00457 ( 41) SS BOND : angle 1.21418 ( 82) hydrogen bonds : bond 0.04297 ( 816) hydrogen bonds : angle 5.68527 ( 2022) link_ALPHA1-2 : bond 0.00322 ( 6) link_ALPHA1-2 : angle 1.79487 ( 18) link_ALPHA1-3 : bond 0.00911 ( 16) link_ALPHA1-3 : angle 1.83370 ( 48) link_ALPHA1-6 : bond 0.00726 ( 14) link_ALPHA1-6 : angle 1.91754 ( 42) link_BETA1-4 : bond 0.00393 ( 58) link_BETA1-4 : angle 2.16694 ( 174) link_NAG-ASN : bond 0.00450 ( 63) link_NAG-ASN : angle 4.07663 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 0.825 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: A 69 TRP cc_start: 0.9038 (m-90) cc_final: 0.8500 (m-90) REVERT: A 95 MET cc_start: 0.7994 (tmm) cc_final: 0.7482 (tmm) REVERT: A 111 LEU cc_start: 0.9310 (mt) cc_final: 0.9078 (mt) REVERT: A 370 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 634 GLU cc_start: 0.8085 (tt0) cc_final: 0.7607 (tp30) REVERT: B 657 GLU cc_start: 0.8931 (mp0) cc_final: 0.8530 (mp0) REVERT: C 150 MET cc_start: 0.9090 (mmm) cc_final: 0.8599 (mpp) REVERT: D 86 LEU cc_start: 0.9211 (mp) cc_final: 0.9010 (mp) REVERT: D 95 MET cc_start: 0.8084 (ttp) cc_final: 0.7667 (ttm) REVERT: D 99 ASN cc_start: 0.8272 (m110) cc_final: 0.8021 (m110) REVERT: D 102 GLU cc_start: 0.8617 (mp0) cc_final: 0.8346 (tt0) REVERT: D 370 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7563 (mt-10) REVERT: D 492 GLU cc_start: 0.8151 (tt0) cc_final: 0.7545 (tm-30) REVERT: E 536 THR cc_start: 0.8644 (p) cc_final: 0.8397 (p) REVERT: E 626 MET cc_start: 0.8017 (ttt) cc_final: 0.7799 (ttt) REVERT: E 651 ASN cc_start: 0.7625 (m110) cc_final: 0.7243 (t0) REVERT: E 655 LYS cc_start: 0.9057 (mttp) cc_final: 0.8809 (mttm) REVERT: F 530 MET cc_start: 0.8394 (ptm) cc_final: 0.7976 (ptm) REVERT: F 579 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8289 (mtm180) REVERT: F 584 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8335 (tm-30) REVERT: F 624 ASP cc_start: 0.8004 (m-30) cc_final: 0.7682 (m-30) REVERT: F 647 GLU cc_start: 0.7754 (tt0) cc_final: 0.7525 (tt0) REVERT: G 31 ASP cc_start: 0.8404 (p0) cc_final: 0.7790 (p0) REVERT: G 54 THR cc_start: 0.8455 (p) cc_final: 0.8219 (p) REVERT: G 80 MET cc_start: 0.8282 (ptm) cc_final: 0.7996 (ptm) REVERT: G 98 ASP cc_start: 0.8972 (m-30) cc_final: 0.8704 (m-30) REVERT: G 100 ASP cc_start: 0.7891 (t0) cc_final: 0.7643 (t0) REVERT: G 100 PHE cc_start: 0.8970 (m-80) cc_final: 0.8645 (m-80) REVERT: H 28 ASN cc_start: 0.8076 (t0) cc_final: 0.7843 (t0) REVERT: H 80 MET cc_start: 0.9174 (tmm) cc_final: 0.8317 (tmm) REVERT: I 23 GLU cc_start: 0.7952 (tp30) cc_final: 0.7448 (tp30) REVERT: I 27 TYR cc_start: 0.9054 (p90) cc_final: 0.8843 (p90) REVERT: I 32 TYR cc_start: 0.8878 (m-10) cc_final: 0.8554 (m-10) REVERT: I 82 LEU cc_start: 0.9317 (mp) cc_final: 0.9116 (mt) REVERT: I 102 VAL cc_start: 0.9056 (m) cc_final: 0.8788 (p) REVERT: J 41 THR cc_start: 0.8751 (m) cc_final: 0.8211 (t) REVERT: J 48 MET cc_start: 0.7749 (mmp) cc_final: 0.7119 (mmm) REVERT: J 50 TRP cc_start: 0.7031 (p-90) cc_final: 0.6725 (p-90) REVERT: J 60 LYS cc_start: 0.7857 (pttm) cc_final: 0.7620 (pttp) REVERT: J 100 TYR cc_start: 0.8351 (t80) cc_final: 0.7641 (t80) REVERT: J 105 LEU cc_start: 0.8520 (mt) cc_final: 0.8302 (mm) REVERT: K 36 TYR cc_start: 0.8871 (m-80) cc_final: 0.7972 (m-10) REVERT: K 42 LYS cc_start: 0.9118 (mttt) cc_final: 0.8822 (mmtm) REVERT: K 65 ARG cc_start: 0.6528 (mtm110) cc_final: 0.6317 (mtm110) REVERT: K 75 ILE cc_start: 0.8835 (mm) cc_final: 0.8531 (mm) REVERT: L 45 LYS cc_start: 0.8753 (tttt) cc_final: 0.8536 (ttpp) REVERT: L 97 PHE cc_start: 0.8881 (m-80) cc_final: 0.8539 (m-80) REVERT: M 36 TYR cc_start: 0.8800 (m-10) cc_final: 0.8298 (m-10) REVERT: M 69 GLN cc_start: 0.7865 (pm20) cc_final: 0.7465 (mp10) REVERT: N 36 TYR cc_start: 0.6785 (m-10) cc_final: 0.6227 (m-10) REVERT: N 37 LEU cc_start: 0.9043 (tt) cc_final: 0.8828 (pt) REVERT: N 47 LEU cc_start: 0.8573 (mp) cc_final: 0.7949 (mp) REVERT: N 79 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7712 (tm-30) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.1559 time to fit residues: 118.2111 Evaluate side-chains 378 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 187 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 43 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.076201 restraints weight = 77724.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078237 restraints weight = 43684.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079612 restraints weight = 29581.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080530 restraints weight = 22756.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081023 restraints weight = 19052.279| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23602 Z= 0.156 Angle : 0.786 19.425 32342 Z= 0.366 Chirality : 0.048 0.466 3977 Planarity : 0.004 0.069 3838 Dihedral : 8.646 59.688 6038 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.04 % Allowed : 0.56 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.31 (0.17), residues: 2589 helix: 0.90 (0.27), residues: 408 sheet: -0.18 (0.17), residues: 848 loop : 0.42 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 542 TYR 0.031 0.002 TYR C 61 PHE 0.041 0.002 PHE H 73 TRP 0.043 0.002 TRP B 571 HIS 0.010 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00346 (23404) covalent geometry : angle 0.70037 (31789) SS BOND : bond 0.00436 ( 41) SS BOND : angle 1.38269 ( 82) hydrogen bonds : bond 0.04158 ( 816) hydrogen bonds : angle 5.62587 ( 2022) link_ALPHA1-2 : bond 0.00297 ( 6) link_ALPHA1-2 : angle 1.79325 ( 18) link_ALPHA1-3 : bond 0.00927 ( 16) link_ALPHA1-3 : angle 1.79291 ( 48) link_ALPHA1-6 : bond 0.00742 ( 14) link_ALPHA1-6 : angle 1.89156 ( 42) link_BETA1-4 : bond 0.00383 ( 58) link_BETA1-4 : angle 2.16400 ( 174) link_NAG-ASN : bond 0.00380 ( 63) link_NAG-ASN : angle 4.03571 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 482 time to evaluate : 0.737 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: A 69 TRP cc_start: 0.9038 (m-90) cc_final: 0.8537 (m-90) REVERT: A 370 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 377 ASN cc_start: 0.9100 (t0) cc_final: 0.8874 (t0) REVERT: A 426 MET cc_start: 0.8701 (tpt) cc_final: 0.8468 (tpp) REVERT: B 542 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7885 (tpt90) REVERT: B 574 LYS cc_start: 0.9289 (mmtp) cc_final: 0.8890 (mttm) REVERT: B 634 GLU cc_start: 0.8091 (tt0) cc_final: 0.7546 (tp30) REVERT: C 150 MET cc_start: 0.9055 (mmm) cc_final: 0.8556 (mpp) REVERT: D 86 LEU cc_start: 0.9211 (mp) cc_final: 0.8997 (mp) REVERT: E 536 THR cc_start: 0.8628 (p) cc_final: 0.8351 (p) REVERT: E 542 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: E 651 ASN cc_start: 0.7602 (m110) cc_final: 0.7159 (t0) REVERT: E 655 LYS cc_start: 0.9013 (mttp) cc_final: 0.8769 (mttm) REVERT: F 530 MET cc_start: 0.8408 (ptm) cc_final: 0.8066 (ptm) REVERT: F 535 MET cc_start: 0.8396 (ptt) cc_final: 0.7501 (tpt) REVERT: F 579 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8150 (mtm180) REVERT: F 584 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 624 ASP cc_start: 0.7990 (m-30) cc_final: 0.7646 (m-30) REVERT: F 647 GLU cc_start: 0.7752 (tt0) cc_final: 0.7255 (tt0) REVERT: G 31 ASP cc_start: 0.8518 (p0) cc_final: 0.8133 (p0) REVERT: G 54 THR cc_start: 0.8472 (p) cc_final: 0.8222 (p) REVERT: G 64 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8717 (mm-40) REVERT: G 72 ASP cc_start: 0.7937 (p0) cc_final: 0.6964 (p0) REVERT: G 98 ASP cc_start: 0.8887 (m-30) cc_final: 0.8676 (m-30) REVERT: G 100 PHE cc_start: 0.8809 (m-80) cc_final: 0.8451 (m-80) REVERT: H 72 ASP cc_start: 0.8569 (p0) cc_final: 0.8252 (p0) REVERT: H 79 TYR cc_start: 0.8777 (m-80) cc_final: 0.8142 (m-10) REVERT: H 80 MET cc_start: 0.9190 (tmm) cc_final: 0.8483 (tmm) REVERT: H 98 ASP cc_start: 0.8617 (t70) cc_final: 0.8281 (t0) REVERT: I 23 GLU cc_start: 0.8075 (tp30) cc_final: 0.7482 (tp30) REVERT: I 27 TYR cc_start: 0.9018 (p90) cc_final: 0.8805 (p90) REVERT: I 32 TYR cc_start: 0.8853 (m-10) cc_final: 0.8555 (m-10) REVERT: I 96 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: I 100 ASP cc_start: 0.8367 (m-30) cc_final: 0.7639 (p0) REVERT: I 102 VAL cc_start: 0.9057 (m) cc_final: 0.8818 (p) REVERT: J 41 THR cc_start: 0.8719 (m) cc_final: 0.8345 (t) REVERT: J 47 TRP cc_start: 0.8131 (t60) cc_final: 0.7852 (t60) REVERT: J 48 MET cc_start: 0.8083 (mmp) cc_final: 0.7531 (mmm) REVERT: J 100 TYR cc_start: 0.8261 (t80) cc_final: 0.7902 (t80) REVERT: J 100 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8378 (mm-30) REVERT: J 100 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8870 (mt-10) REVERT: K 5 THR cc_start: 0.8055 (p) cc_final: 0.7668 (p) REVERT: K 36 TYR cc_start: 0.8740 (m-80) cc_final: 0.7830 (m-10) REVERT: K 65 ARG cc_start: 0.6527 (mtm110) cc_final: 0.6266 (mtm110) REVERT: K 75 ILE cc_start: 0.8884 (mm) cc_final: 0.8571 (mm) REVERT: K 82 ASP cc_start: 0.7909 (m-30) cc_final: 0.7417 (m-30) REVERT: L 45 LYS cc_start: 0.8733 (tttt) cc_final: 0.8518 (ttpp) REVERT: L 97 PHE cc_start: 0.8835 (m-80) cc_final: 0.8580 (m-80) REVERT: M 36 TYR cc_start: 0.8686 (m-10) cc_final: 0.8250 (m-10) REVERT: M 69 GLN cc_start: 0.7921 (pm20) cc_final: 0.7661 (mp10) REVERT: N 36 TYR cc_start: 0.6632 (m-10) cc_final: 0.6180 (m-10) REVERT: N 37 LEU cc_start: 0.9084 (tt) cc_final: 0.8832 (pt) REVERT: N 47 LEU cc_start: 0.8581 (mp) cc_final: 0.8182 (mp) REVERT: N 61 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7532 (ptt180) outliers start: 1 outliers final: 0 residues processed: 483 average time/residue: 0.1398 time to fit residues: 106.2968 Evaluate side-chains 377 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 201 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 168 optimal weight: 0.2980 chunk 206 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.092633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075623 restraints weight = 77964.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077612 restraints weight = 44029.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078946 restraints weight = 30043.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079841 restraints weight = 23228.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080400 restraints weight = 19529.385| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23602 Z= 0.188 Angle : 0.820 17.574 32342 Z= 0.384 Chirality : 0.048 0.388 3977 Planarity : 0.005 0.069 3838 Dihedral : 8.557 59.126 6038 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.09 % Allowed : 0.30 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.25 (0.17), residues: 2589 helix: 0.99 (0.27), residues: 401 sheet: -0.23 (0.17), residues: 836 loop : 0.34 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 480 TYR 0.018 0.002 TYR H 99 PHE 0.027 0.002 PHE C 391 TRP 0.073 0.002 TRP A 96 HIS 0.012 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00421 (23404) covalent geometry : angle 0.73925 (31789) SS BOND : bond 0.00479 ( 41) SS BOND : angle 1.39704 ( 82) hydrogen bonds : bond 0.04207 ( 816) hydrogen bonds : angle 5.60148 ( 2022) link_ALPHA1-2 : bond 0.00300 ( 6) link_ALPHA1-2 : angle 1.80519 ( 18) link_ALPHA1-3 : bond 0.00886 ( 16) link_ALPHA1-3 : angle 1.85739 ( 48) link_ALPHA1-6 : bond 0.00711 ( 14) link_ALPHA1-6 : angle 1.87231 ( 42) link_BETA1-4 : bond 0.00392 ( 58) link_BETA1-4 : angle 2.18109 ( 174) link_NAG-ASN : bond 0.00415 ( 63) link_NAG-ASN : angle 3.98635 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 475 time to evaluate : 0.639 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: A 69 TRP cc_start: 0.9073 (m-90) cc_final: 0.8548 (m-90) REVERT: A 111 LEU cc_start: 0.9199 (mt) cc_final: 0.8983 (mt) REVERT: A 356 ASN cc_start: 0.7640 (m-40) cc_final: 0.7205 (p0) REVERT: A 370 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 426 MET cc_start: 0.8883 (tpt) cc_final: 0.8652 (tpp) REVERT: B 574 LYS cc_start: 0.9264 (mmtp) cc_final: 0.8830 (mttm) REVERT: B 634 GLU cc_start: 0.8099 (tt0) cc_final: 0.7586 (tp30) REVERT: C 150 MET cc_start: 0.9051 (mmm) cc_final: 0.8683 (mpp) REVERT: C 434 MET cc_start: 0.8765 (tpp) cc_final: 0.8467 (tpt) REVERT: D 86 LEU cc_start: 0.9230 (mp) cc_final: 0.8918 (mp) REVERT: E 536 THR cc_start: 0.8670 (p) cc_final: 0.8431 (p) REVERT: E 651 ASN cc_start: 0.7607 (m110) cc_final: 0.7137 (t0) REVERT: E 655 LYS cc_start: 0.9024 (mttp) cc_final: 0.8720 (mttm) REVERT: F 530 MET cc_start: 0.8372 (ptm) cc_final: 0.7954 (ptm) REVERT: F 579 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8196 (mtm180) REVERT: F 584 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8319 (tm-30) REVERT: F 624 ASP cc_start: 0.8046 (m-30) cc_final: 0.7718 (m-30) REVERT: F 647 GLU cc_start: 0.7748 (tt0) cc_final: 0.7544 (tt0) REVERT: G 64 GLN cc_start: 0.8930 (mm-40) cc_final: 0.7572 (mm110) REVERT: G 72 ASP cc_start: 0.7966 (p0) cc_final: 0.7374 (p0) REVERT: G 100 PHE cc_start: 0.8894 (m-80) cc_final: 0.8599 (m-80) REVERT: H 72 ASP cc_start: 0.8421 (p0) cc_final: 0.8082 (p0) REVERT: H 79 TYR cc_start: 0.8786 (m-80) cc_final: 0.8136 (m-10) REVERT: H 80 MET cc_start: 0.9229 (tmm) cc_final: 0.8504 (tmm) REVERT: H 98 ASP cc_start: 0.8631 (t70) cc_final: 0.8404 (t0) REVERT: I 23 GLU cc_start: 0.8075 (tp30) cc_final: 0.7671 (tp30) REVERT: I 27 TYR cc_start: 0.9089 (p90) cc_final: 0.8848 (p90) REVERT: I 32 TYR cc_start: 0.8855 (m-10) cc_final: 0.8510 (m-10) REVERT: I 76 TYR cc_start: 0.8293 (m-10) cc_final: 0.8084 (m-10) REVERT: I 102 VAL cc_start: 0.9065 (m) cc_final: 0.8784 (p) REVERT: J 41 THR cc_start: 0.8584 (m) cc_final: 0.8128 (t) REVERT: J 47 TRP cc_start: 0.8108 (t60) cc_final: 0.7764 (t60) REVERT: J 48 MET cc_start: 0.8007 (mmp) cc_final: 0.7538 (mmm) REVERT: J 50 TRP cc_start: 0.6728 (p-90) cc_final: 0.6480 (p-90) REVERT: J 100 TYR cc_start: 0.8370 (t80) cc_final: 0.7696 (t80) REVERT: J 100 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8302 (mm-30) REVERT: K 5 THR cc_start: 0.7948 (p) cc_final: 0.7448 (p) REVERT: K 36 TYR cc_start: 0.8808 (m-80) cc_final: 0.8007 (m-10) REVERT: K 75 ILE cc_start: 0.8883 (mm) cc_final: 0.8535 (mm) REVERT: K 82 ASP cc_start: 0.7945 (m-30) cc_final: 0.7657 (m-30) REVERT: L 45 LYS cc_start: 0.8738 (tttt) cc_final: 0.8535 (ttpp) REVERT: L 97 PHE cc_start: 0.8855 (m-80) cc_final: 0.8603 (m-80) REVERT: M 36 TYR cc_start: 0.8796 (m-10) cc_final: 0.8292 (m-10) REVERT: M 69 GLN cc_start: 0.8045 (pm20) cc_final: 0.7819 (mp10) outliers start: 2 outliers final: 0 residues processed: 476 average time/residue: 0.1454 time to fit residues: 108.6275 Evaluate side-chains 376 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 188 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 121 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 330 HIS ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.077141 restraints weight = 77389.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079075 restraints weight = 44899.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080369 restraints weight = 31060.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081250 restraints weight = 24192.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081717 restraints weight = 20368.099| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23602 Z= 0.142 Angle : 0.784 17.169 32342 Z= 0.368 Chirality : 0.048 0.397 3977 Planarity : 0.004 0.068 3838 Dihedral : 8.120 57.074 6038 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.09 % Allowed : 0.22 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.29 (0.17), residues: 2589 helix: 1.04 (0.27), residues: 400 sheet: -0.14 (0.17), residues: 844 loop : 0.32 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.031 0.002 TYR C 61 PHE 0.025 0.002 PHE H 73 TRP 0.050 0.002 TRP B 571 HIS 0.011 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00315 (23404) covalent geometry : angle 0.70617 (31789) SS BOND : bond 0.00464 ( 41) SS BOND : angle 1.33742 ( 82) hydrogen bonds : bond 0.04063 ( 816) hydrogen bonds : angle 5.54035 ( 2022) link_ALPHA1-2 : bond 0.00304 ( 6) link_ALPHA1-2 : angle 1.79276 ( 18) link_ALPHA1-3 : bond 0.00916 ( 16) link_ALPHA1-3 : angle 1.79699 ( 48) link_ALPHA1-6 : bond 0.00715 ( 14) link_ALPHA1-6 : angle 1.78670 ( 42) link_BETA1-4 : bond 0.00387 ( 58) link_BETA1-4 : angle 2.12546 ( 174) link_NAG-ASN : bond 0.00340 ( 63) link_NAG-ASN : angle 3.82228 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.01 seconds wall clock time: 66 minutes 13.84 seconds (3973.84 seconds total)