Starting phenix.real_space_refine on Sun Sep 13 07:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vy2_21456/09_2026/6vy2_21456.cif" } resolution = 4.86 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= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 13296 2.51 5 N 3456 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "N" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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 chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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 chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 chiralities: 3 Chain: "Y" 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 chiralities: 7 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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 chiralities: 5 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "j" 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 chiralities: 5 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 chiralities: 2 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" 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 chiralities: 7 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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 chiralities: 5 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 chiralities: 3 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "z" 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 chiralities: 5 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "4" 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 chiralities: 7 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 3 Chain: "C" 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 chiralities: 5 Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 5 Chain: "F" 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 chiralities: 3 Time building chain proxies: 4.99, per 1000 atoms: 0.23 Number of scatterers: 21426 At special positions: 0 Unit cell: (151.96, 148.48, 131.08, 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 132 16.00 O 4542 8.00 N 3456 7.00 C 13296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=1.84 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.12 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM20874 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 4 3 " - " MAN 4 4 " " MAN 4 4 " - " MAN 4 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 4 " " MAN o 4 " - " MAN o 5 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA 4 3 " - " MAN 4 6 " " MAN 4 6 " - " MAN 4 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 6 " - " MAN Y 7 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 6 " " MAN o 6 " - " MAN o 7 " " BMA w 3 " - " MAN w 4 " " MAN w 4 " - " MAN w 5 " " BMA z 3 " - " MAN z 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 V 2 " - " BMA V 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " 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 t 1 " - " NAG t 2 " " 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 w 2 " - " BMA w 3 " " 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 z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 276 " " NAG 1 1 " - " ASN E 289 " " NAG 2 1 " - " ASN E 334 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 386 " " NAG 5 1 " - " ASN E 392 " " NAG 6 1 " - " ASN E 448 " " NAG 7 1 " - " ASN E 461 " " NAG A 608 " - " ASN A 156 " " NAG A 611 " - " ASN A 187 " " NAG A 635 " - " ASN A 301 " " NAG A 641 " - " ASN A 358 " " NAG A 652 " - " ASN A 442 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 608 " - " ASN C 156 " " NAG C 611 " - " ASN C 187 " " NAG C 635 " - " ASN C 301 " " NAG C 641 " - " ASN C 358 " " NAG C 652 " - " ASN C 442 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 608 " - " ASN E 156 " " NAG E 611 " - " ASN E 187 " " NAG E 635 " - " ASN E 301 " " NAG E 641 " - " ASN E 358 " " NAG E 652 " - " ASN E 442 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 136 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 230 " " NAG S 1 " - " ASN A 241 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 289 " " NAG W 1 " - " ASN A 334 " " NAG X 1 " - " ASN A 339 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 461 " " NAG c 1 " - " ASN C 88 " " NAG d 1 " - " ASN C 130 " " NAG e 1 " - " ASN C 136 " " NAG f 1 " - " ASN C 160 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 230 " " NAG i 1 " - " ASN C 241 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 289 " " NAG m 1 " - " ASN C 334 " " NAG n 1 " - " ASN C 339 " " NAG o 1 " - " ASN C 386 " " NAG p 1 " - " ASN C 392 " " NAG q 1 " - " ASN C 448 " " NAG r 1 " - " ASN C 461 " " NAG s 1 " - " ASN E 88 " " NAG t 1 " - " ASN E 130 " " NAG u 1 " - " ASN E 136 " " NAG v 1 " - " ASN E 160 " " NAG w 1 " - " ASN E 197 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN E 262 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 885.4 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 22.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.007A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.212A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.822A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.943A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.518A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.833A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 649 removed outlier: 5.127A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'C' and resid 100 through 116 removed outlier: 4.006A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.211A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.822A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.945A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 removed outlier: 3.518A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.832A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 649 removed outlier: 5.127A pdb=" N ASN D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 663 Processing helix chain 'E' and resid 100 through 116 removed outlier: 4.007A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.212A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.823A pdb=" N ASN E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.944A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 544 removed outlier: 3.519A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 597 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.833A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 649 removed outlier: 5.129A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 663 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'L' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR L 27B" --> pdb=" O ILE L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 26 through 27B' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR M 27B" --> pdb=" O ILE M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 26 through 27B' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR N 27B" --> pdb=" O ILE N 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 26 through 27B' Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.331A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (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 92 removed outlier: 3.521A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.344A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.349A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.010A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.077A pdb=" N ASN A 301 " --> pdb=" O VAL A 322A" (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.321A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.851A 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 92 removed outlier: 3.520A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.343A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.347A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL C 292 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS C 293 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 334 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 7.011A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL C 292 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 359 " --> pdb=" O TYR C 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.078A pdb=" N ASN C 301 " --> pdb=" O VAL C 322A" (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.217A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.792A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.520A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.344A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.348A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS E 293 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 7.010A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 359 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 312 removed outlier: 7.078A pdb=" N ASN E 301 " --> pdb=" O VAL E 322A" (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 322A" --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.504A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR H 33 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.504A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG H 94 " --> pdb=" O LEU H 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H 100J" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU H 96 " --> pdb=" O SER H 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP H 100 " --> pdb=" O LEU H 100D" (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU H 100D" --> pdb=" O TRP H 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.234A pdb=" N TYR I 33 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.979A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG I 94 " --> pdb=" O LEU I 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU I 100J" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU I 96 " --> pdb=" O SER I 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP I 100 " --> pdb=" O LEU I 100D" (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU I 100D" --> pdb=" O TRP I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.233A pdb=" N TYR J 33 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.979A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG J 94 " --> pdb=" O LEU J 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU J 100J" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU J 96 " --> pdb=" O SER J 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP J 100 " --> pdb=" O LEU J 100D" (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU J 100D" --> pdb=" O TRP J 100 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.493A pdb=" N VAL L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.495A pdb=" N VAL M 33 " --> pdb=" O LYS M 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.496A pdb=" N VAL N 33 " --> pdb=" O LYS N 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 13 Processing sheet with id=AE9, first strand: chain 'N' and resid 19 through 24 780 hydrogen bonds defined for protein. 1977 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: 4.23 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6477 1.34 - 1.46: 5754 1.46 - 1.59: 9414 1.59 - 1.71: 0 1.71 - 1.83: 186 Bond restraints: 21831 Sorted by residual: bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 NAG A 611 " pdb=" O5 NAG A 611 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C1 NAG E 611 " pdb=" O5 NAG E 611 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 21826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 27674 2.02 - 4.04: 1469 4.04 - 6.06: 389 6.06 - 8.08: 87 8.08 - 10.09: 12 Bond angle restraints: 29631 Sorted by residual: angle pdb=" N MET A 154 " pdb=" CA MET A 154 " pdb=" C MET A 154 " ideal model delta sigma weight residual 110.97 117.08 -6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N MET C 154 " pdb=" CA MET C 154 " pdb=" C MET C 154 " ideal model delta sigma weight residual 110.97 117.04 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N MET E 154 " pdb=" CA MET E 154 " pdb=" C MET E 154 " ideal model delta sigma weight residual 110.97 117.00 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" C ASN E 195 " pdb=" N CYS E 196 " pdb=" CA CYS E 196 " ideal model delta sigma weight residual 121.66 112.67 8.99 1.76e+00 3.23e-01 2.61e+01 angle pdb=" C ASN A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta sigma weight residual 121.66 112.69 8.97 1.76e+00 3.23e-01 2.60e+01 ... (remaining 29626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10585 17.58 - 35.17: 821 35.17 - 52.75: 204 52.75 - 70.33: 69 70.33 - 87.92: 21 Dihedral angle restraints: 11700 sinusoidal: 4677 harmonic: 7023 Sorted by residual: dihedral pdb=" CA THR E 406 " pdb=" C THR E 406 " pdb=" N GLU E 407 " pdb=" CA GLU E 407 " ideal model delta harmonic sigma weight residual 180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA THR A 406 " pdb=" C THR A 406 " pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta harmonic sigma weight residual -180.00 -125.66 -54.34 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA THR C 406 " pdb=" C THR C 406 " pdb=" N GLU C 407 " pdb=" CA GLU C 407 " ideal model delta harmonic sigma weight residual -180.00 -125.70 -54.30 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 11697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 3757 0.193 - 0.386: 54 0.386 - 0.579: 13 0.579 - 0.772: 4 0.772 - 0.965: 9 Chirality restraints: 3837 Sorted by residual: chirality pdb=" C1 NAG w 1 " pdb=" ND2 ASN E 197 " pdb=" C2 NAG w 1 " pdb=" O5 NAG w 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 618 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 3834 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 618 " -0.016 2.00e-02 2.50e+03 1.06e-01 1.40e+02 pdb=" CG ASN F 618 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN F 618 " 0.110 2.00e-02 2.50e+03 pdb=" ND2 ASN F 618 " -0.170 2.00e-02 2.50e+03 pdb=" C1 NAG F 702 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 160 " 0.077 2.00e-02 2.50e+03 8.47e-02 8.96e+01 pdb=" CG ASN E 160 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 160 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN E 160 " -0.134 2.00e-02 2.50e+03 pdb=" C1 NAG v 1 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 156 " 0.074 2.00e-02 2.50e+03 7.86e-02 7.73e+01 pdb=" CG ASN E 156 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 156 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN E 156 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG E 608 " 0.097 2.00e-02 2.50e+03 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 546 2.63 - 3.19: 20229 3.19 - 3.76: 32967 3.76 - 4.33: 44578 4.33 - 4.90: 69159 Nonbonded interactions: 167479 Sorted by model distance: nonbonded pdb=" N ASP C 185 " pdb=" OD1 ASP C 185 " model vdw 2.056 3.120 nonbonded pdb=" N ASP E 185 " pdb=" OD1 ASP E 185 " model vdw 2.058 3.120 nonbonded pdb=" N ASP A 185 " pdb=" OD1 ASP A 185 " model vdw 2.059 3.120 nonbonded pdb=" OH TYR C 384 " pdb=" OH TYR I 100A" model vdw 2.082 3.040 nonbonded pdb=" NE ARG E 393 " pdb=" O7 NAG 3 1 " model vdw 2.116 3.120 ... (remaining 167474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '5' selection = chain '6' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '7' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain '4' selection = chain 'Y' selection = chain 'o' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'S' selection = chain 'i' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 9 pdb_interpretation.ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '5' selection = chain '6' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'x' } pdb_interpretation.ncs_group { reference = chain '2' selection = chain '7' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain '4' selection = chain 'Y' selection = chain 'o' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 'i' selection = chain 'y' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.009 0.315 22044 Z= 0.455 Angle : 1.364 27.806 30237 Z= 0.602 Chirality : 0.081 0.965 3837 Planarity : 0.004 0.071 3516 Dihedral : 14.486 87.915 7095 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.68 % Favored : 93.82 % Rotamer: Outliers : 4.96 % Allowed : 6.89 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.15), residues: 2412 helix: -2.12 (0.20), residues: 393 sheet: -0.70 (0.19), residues: 672 loop : -1.94 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 469 TYR 0.015 0.002 TYR E 217 PHE 0.011 0.002 PHE E 383 TRP 0.019 0.002 TRP H 100 HIS 0.003 0.001 HIS E 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.35 (21831) covalent geometry : angle 1.11211 / 0.54 (29631) SS BOND : bond 0.03671 / 2.09 ( 33) SS BOND : angle 3.08246 / 2.19 ( 66) hydrogen bonds : bond 0.15341 / 10.24 ( 726) hydrogen bonds : angle 7.46453 / 5.26 ( 1977) link_ALPHA1-3 : bond 0.00783 / 0.47 ( 12) link_ALPHA1-3 : angle 1.98995 / 1.25 ( 36) link_ALPHA1-6 : bond 0.00527 / 0.32 ( 15) link_ALPHA1-6 : angle 1.87302 / 1.14 ( 45) link_BETA1-4 : bond 0.00952 / 0.68 ( 81) link_BETA1-4 : angle 3.63101 / 2.51 ( 243) link_NAG-ASN : bond 0.09895 / 5.36 ( 72) link_NAG-ASN : angle 8.45718 / 5.84 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9328 (m-30) cc_final: 0.9094 (p0) REVERT: A 108 VAL cc_start: 0.9768 (t) cc_final: 0.9326 (p) REVERT: A 193 LEU cc_start: 0.9727 (tp) cc_final: 0.9381 (tp) REVERT: A 259 LEU cc_start: 0.9363 (mt) cc_final: 0.8921 (mt) REVERT: A 368 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 426 MET cc_start: 0.8774 (mtp) cc_final: 0.8396 (ttm) REVERT: A 434 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8810 (ptp) outliers start: 21 outliers final: 3 residues processed: 79 average time/residue: 0.0663 time to fit residues: 6.6045 Evaluate side-chains 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.156 Evaluate side-chains 49 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.043 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: B 580 VAL cc_start: 0.9814 (t) cc_final: 0.9609 (m) REVERT: B 581 LEU cc_start: 0.9806 (tp) cc_final: 0.9483 (tp) REVERT: B 584 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8522 (mt-10) REVERT: B 587 LEU cc_start: 0.9680 (mm) cc_final: 0.9410 (pp) REVERT: B 639 THR cc_start: 0.8418 (p) cc_final: 0.7705 (p) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.0958 time to fit residues: 4.7658 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.040 Evaluate side-chains 43 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8903 (mmm) cc_final: 0.8682 (mmm) REVERT: H 37 LEU cc_start: 0.8421 (mp) cc_final: 0.7780 (tt) REVERT: H 51 MET cc_start: 0.9506 (ttp) cc_final: 0.9092 (tmm) REVERT: H 58 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8795 (p) REVERT: H 72 ASP cc_start: 0.9401 (t0) cc_final: 0.8782 (p0) outliers start: 7 outliers final: 1 residues processed: 40 average time/residue: 0.0475 time to fit residues: 2.1237 Evaluate side-chains 20 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.040 Evaluate side-chains 32 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 MET cc_start: 0.8184 (mmm) cc_final: 0.7761 (mmm) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.0677 time to fit residues: 2.2659 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.052961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.048239 restraints weight = 496.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.048687 restraints weight = 351.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.049521 restraints weight = 281.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.051636 restraints weight = 244.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.052269 restraints weight = 105.104| |-----------------------------------------------------------------------------| r_work (final): 0.2636 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.039315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.037576 restraints weight = 540.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.037912 restraints weight = 208.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.038142 restraints weight = 137.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.038344 restraints weight = 101.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.038343 restraints weight = 76.836| |-----------------------------------------------------------------------------| r_work (final): 0.2357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051611 restraints weight = 819.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052679 restraints weight = 585.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053533 restraints weight = 453.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054123 restraints weight = 370.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.054475 restraints weight = 310.109| |-----------------------------------------------------------------------------| r_work (final): 0.2823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035518 restraints weight = 24711.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.037030 restraints weight = 16022.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.038189 restraints weight = 11564.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.039076 restraints weight = 8986.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.039746 restraints weight = 7355.659| |-----------------------------------------------------------------------------| r_work (final): 0.2842 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.034031 restraints weight = 7753.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.035336 restraints weight = 4664.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.036203 restraints weight = 3270.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.036817 restraints weight = 2526.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.037352 restraints weight = 2079.643| |-----------------------------------------------------------------------------| r_work (final): 0.2689 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.031378 restraints weight = 7208.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.032733 restraints weight = 4371.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.033736 restraints weight = 3089.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.034511 restraints weight = 2374.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.035001 restraints weight = 1937.762| |-----------------------------------------------------------------------------| r_work (final): 0.2650 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.027996 restraints weight = 5610.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.029496 restraints weight = 3155.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.030628 restraints weight = 2068.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.031474 restraints weight = 1478.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.032081 restraints weight = 1129.619| |-----------------------------------------------------------------------------| r_work (final): 0.2533 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.049330 restraints weight = 702.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.050279 restraints weight = 252.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.050816 restraints weight = 119.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.051126 restraints weight = 64.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051322 restraints weight = 35.945| |-----------------------------------------------------------------------------| r_work (final): 0.2721 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.046365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.040026 restraints weight = 804.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.040283 restraints weight = 580.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.040283 restraints weight = 525.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.040283 restraints weight = 525.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.040283 restraints weight = 525.529| |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.651 22044 Z= 0.858 Angle : 2.586 50.803 30237 Z= 0.979 Chirality : 0.131 1.698 3837 Planarity : 0.007 0.095 3516 Dihedral : 7.415 53.620 2634 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.66 % Rotamer: Outliers : 1.27 % Allowed : 5.38 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2412 helix: -1.59 (0.23), residues: 393 sheet: -0.56 (0.19), residues: 654 loop : -1.92 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 393 TYR 0.069 0.004 TYR J 100G PHE 0.040 0.003 PHE M 32 TRP 0.053 0.003 TRP B 571 HIS 0.007 0.001 HIS L 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01192 / 0.54 (21831) covalent geometry : angle 2.17578 / 0.86 (29631) SS BOND : bond 0.06825 / 4.51 ( 33) SS BOND : angle 2.91768 / 2.20 ( 66) hydrogen bonds : bond 0.07367 / 4.81 ( 726) hydrogen bonds : angle 7.00804 / 4.98 ( 1977) link_ALPHA1-3 : bond 0.18260 / 10.65 ( 12) link_ALPHA1-3 : angle 15.09333 / 9.64 ( 36) link_ALPHA1-6 : bond 0.45337 / 26.97 ( 15) link_ALPHA1-6 : angle 21.35835 / 14.38 ( 45) link_BETA1-4 : bond 0.02738 / 1.59 ( 81) link_BETA1-4 : angle 5.35294 / 3.59 ( 243) link_NAG-ASN : bond 0.05424 / 3.54 ( 72) link_NAG-ASN : angle 10.91112 / 7.53 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.133 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: A 95 MET cc_start: 0.9487 (ppp) cc_final: 0.9261 (ppp) REVERT: A 107 ASP cc_start: 0.9328 (m-30) cc_final: 0.9103 (m-30) REVERT: A 176 PHE cc_start: 0.9438 (m-80) cc_final: 0.9210 (m-80) REVERT: A 193 LEU cc_start: 0.9719 (tp) cc_final: 0.9371 (tp) REVERT: A 381 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9117 (mp0) REVERT: A 383 PHE cc_start: 0.9791 (m-80) cc_final: 0.9263 (m-80) REVERT: A 434 MET cc_start: 0.9665 (ttp) cc_final: 0.9389 (ppp) REVERT: A 453 LEU cc_start: 0.9562 (tp) cc_final: 0.9214 (tp) REVERT: A 475 MET cc_start: 0.7819 (tpt) cc_final: 0.7354 (tpp) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.0738 time to fit residues: 4.3277 Evaluate side-chains 35 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.149 Evaluate side-chains 33 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8865 (mtp) cc_final: 0.8310 (mmt) REVERT: B 584 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8699 (mt-10) REVERT: B 639 THR cc_start: 0.8813 (p) cc_final: 0.8362 (p) REVERT: B 643 TYR cc_start: 0.9392 (m-80) cc_final: 0.9172 (m-80) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0885 time to fit residues: 3.1170 Evaluate side-chains 23 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.049 Evaluate side-chains 30 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.040 Fit side-chains REVERT: I 37 LEU cc_start: 0.8605 (mp) cc_final: 0.8386 (tp) REVERT: I 51 MET cc_start: 0.9443 (ttp) cc_final: 0.9005 (tmm) REVERT: I 100 ASP cc_start: 0.9411 (t0) cc_final: 0.9202 (m-30) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.0417 time to fit residues: 1.3923 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.033 Evaluate side-chains 20 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.028 Fit side-chains revert: symmetry clash REVERT: L 48 MET cc_start: 0.7788 (mmm) cc_final: 0.7569 (mmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0571 time to fit residues: 1.2671 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.040 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 0.0470 chunk 172 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.042874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.036870 restraints weight = 612.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.037754 restraints weight = 391.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.038116 restraints weight = 319.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.038116 restraints weight = 287.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.038116 restraints weight = 287.979| |-----------------------------------------------------------------------------| r_work (final): 0.2478 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.045694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.042126 restraints weight = 259.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.042853 restraints weight = 157.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.043543 restraints weight = 110.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.044049 restraints weight = 67.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.044432 restraints weight = 49.718| |-----------------------------------------------------------------------------| r_work (final): 0.2298 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.059385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.056423 restraints weight = 717.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057010 restraints weight = 415.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057369 restraints weight = 299.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.057658 restraints weight = 226.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057827 restraints weight = 184.121| |-----------------------------------------------------------------------------| r_work (final): 0.2963 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035020 restraints weight = 24568.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036505 restraints weight = 16074.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037641 restraints weight = 11613.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.038561 restraints weight = 9037.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039274 restraints weight = 7372.905| |-----------------------------------------------------------------------------| r_work (final): 0.2831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042027 restraints weight = 9078.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043381 restraints weight = 5022.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044297 restraints weight = 3255.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044933 restraints weight = 2401.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045359 restraints weight = 1920.992| |-----------------------------------------------------------------------------| r_work (final): 0.3052 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.040509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.030910 restraints weight = 7003.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.032124 restraints weight = 4447.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.033057 restraints weight = 3230.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.033667 restraints weight = 2526.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.034241 restraints weight = 2130.292| |-----------------------------------------------------------------------------| r_work (final): 0.2627 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.038492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.030039 restraints weight = 5628.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.031635 restraints weight = 2971.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.032762 restraints weight = 1973.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.033530 restraints weight = 1433.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.034286 restraints weight = 1137.333| |-----------------------------------------------------------------------------| r_work (final): 0.2579 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.051431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.050647 restraints weight = 711.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.051092 restraints weight = 171.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051306 restraints weight = 58.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.051371 restraints weight = 21.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051398 restraints weight = 7.819 | |-----------------------------------------------------------------------------| r_work (final): 0.2723 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.046287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.039923 restraints weight = 734.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.040180 restraints weight = 523.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.040180 restraints weight = 471.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.040180 restraints weight = 471.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.040180 restraints weight = 471.932| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.623 22044 Z= 0.802 Angle : 2.146 45.670 30237 Z= 0.831 Chirality : 0.124 1.750 3837 Planarity : 0.006 0.057 3516 Dihedral : 7.648 54.065 2634 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.34 % Favored : 93.28 % Rotamer: Outliers : 0.28 % Allowed : 4.25 % Favored : 95.47 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 2412 helix: -1.33 (0.24), residues: 393 sheet: -0.51 (0.19), residues: 654 loop : -1.98 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 308 TYR 0.044 0.003 TYR I 100G PHE 0.101 0.005 PHE M 32 TRP 0.049 0.003 TRP H 47 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00983 / 0.43 (21831) covalent geometry : angle 1.69397 / 0.71 (29631) SS BOND : bond 0.06604 / 4.54 ( 33) SS BOND : angle 2.86895 / 2.08 ( 66) hydrogen bonds : bond 0.06569 / 4.26 ( 726) hydrogen bonds : angle 6.93330 / 4.95 ( 1977) link_ALPHA1-3 : bond 0.24651 / 14.38 ( 12) link_ALPHA1-3 : angle 13.08988 / 7.52 ( 36) link_ALPHA1-6 : bond 0.44423 / 26.47 ( 15) link_ALPHA1-6 : angle 21.02329 / 13.65 ( 45) link_BETA1-4 : bond 0.01378 / 0.81 ( 81) link_BETA1-4 : angle 2.89004 / 1.95 ( 243) link_NAG-ASN : bond 0.05504 / 3.48 ( 72) link_NAG-ASN : angle 10.88412 / 7.37 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 39 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9503 (ppp) cc_final: 0.9216 (ppp) REVERT: A 107 ASP cc_start: 0.9379 (m-30) cc_final: 0.9155 (m-30) REVERT: A 129 LEU cc_start: 0.9475 (tp) cc_final: 0.9269 (tp) REVERT: A 383 PHE cc_start: 0.9785 (m-80) cc_final: 0.9357 (m-80) REVERT: A 453 LEU cc_start: 0.9570 (tp) cc_final: 0.9247 (tp) REVERT: A 475 MET cc_start: 0.7823 (tpt) cc_final: 0.7301 (tpp) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0696 time to fit residues: 3.4748 Evaluate side-chains 28 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.140 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 643 TYR cc_start: 0.9395 (m-80) cc_final: 0.9180 (m-80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0812 time to fit residues: 2.6114 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.039 Evaluate side-chains 25 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.040 Fit side-chains REVERT: I 51 MET cc_start: 0.9514 (ttp) cc_final: 0.8970 (tmm) REVERT: I 72 ASP cc_start: 0.9246 (t70) cc_final: 0.8862 (p0) REVERT: I 82 MET cc_start: 0.9376 (pmm) cc_final: 0.9176 (pmm) REVERT: I 100 ASP cc_start: 0.9204 (t0) cc_final: 0.8824 (m-30) REVERT: I 100 TYR cc_start: 0.8976 (p90) cc_final: 0.8553 (p90) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0265 time to fit residues: 0.8103 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.040 Evaluate side-chains 20 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: M 48 MET cc_start: 0.8208 (mmm) cc_final: 0.7640 (mmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0489 time to fit residues: 1.0922 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.0170 chunk 100 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 0.0770 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.046522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 14)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.037787 restraints weight = 548.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038453 restraints weight = 418.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038453 restraints weight = 363.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038453 restraints weight = 363.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038453 restraints weight = 363.045| |-----------------------------------------------------------------------------| r_work (final): 0.2492 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.044147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.041318 restraints weight = 324.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.042001 restraints weight = 181.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.042706 restraints weight = 119.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.043062 restraints weight = 67.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.043406 restraints weight = 47.770| |-----------------------------------------------------------------------------| r_work (final): 0.2251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056896 restraints weight = 866.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057758 restraints weight = 535.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058372 restraints weight = 345.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058639 restraints weight = 235.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058871 restraints weight = 190.277| |-----------------------------------------------------------------------------| r_work (final): 0.2973 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.034899 restraints weight = 24289.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.036379 restraints weight = 15804.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.037527 restraints weight = 11481.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038430 restraints weight = 8954.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039137 restraints weight = 7294.293| |-----------------------------------------------------------------------------| r_work (final): 0.2835 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.043163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.035191 restraints weight = 10061.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.036477 restraints weight = 5961.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.037341 restraints weight = 4118.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.037966 restraints weight = 3155.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.038405 restraints weight = 2576.419| |-----------------------------------------------------------------------------| r_work (final): 0.2643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032803 restraints weight = 6968.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.034131 restraints weight = 4256.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.035105 restraints weight = 2999.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.035756 restraints weight = 2288.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.036397 restraints weight = 1853.189| |-----------------------------------------------------------------------------| r_work (final): 0.2670 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.036299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.027757 restraints weight = 5629.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.029287 restraints weight = 3184.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.030489 restraints weight = 2129.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.031315 restraints weight = 1555.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.032107 restraints weight = 1220.706| |-----------------------------------------------------------------------------| r_work (final): 0.2490 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050239 restraints weight = 739.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050884 restraints weight = 245.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.051286 restraints weight = 118.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.051478 restraints weight = 61.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051583 restraints weight = 33.978| |-----------------------------------------------------------------------------| r_work (final): 0.2757 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.046751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.040264 restraints weight = 720.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.040576 restraints weight = 505.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.040643 restraints weight = 450.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.040900 restraints weight = 441.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.041163 restraints weight = 411.858| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.579 22044 Z= 0.724 Angle : 1.992 47.403 30237 Z= 0.776 Chirality : 0.140 3.162 3837 Planarity : 0.006 0.057 3516 Dihedral : 7.584 54.097 2634 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 2412 helix: -1.07 (0.24), residues: 393 sheet: -0.47 (0.19), residues: 657 loop : -2.08 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 588 TYR 0.035 0.003 TYR J 100A PHE 0.050 0.003 PHE L 95B TRP 0.019 0.002 TRP I 47 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.32 (21831) covalent geometry : angle 1.53542 / 0.65 (29631) SS BOND : bond 0.06548 / 4.46 ( 33) SS BOND : angle 2.81198 / 2.04 ( 66) hydrogen bonds : bond 0.05777 / 3.72 ( 726) hydrogen bonds : angle 6.83310 / 4.87 ( 1977) link_ALPHA1-3 : bond 0.23714 / 13.83 ( 12) link_ALPHA1-3 : angle 11.51677 / 6.31 ( 36) link_ALPHA1-6 : bond 0.42139 / 25.05 ( 15) link_ALPHA1-6 : angle 20.97264 / 13.46 ( 45) link_BETA1-4 : bond 0.01126 / 0.67 ( 81) link_BETA1-4 : angle 2.71802 / 1.92 ( 243) link_NAG-ASN : bond 0.05743 / 3.49 ( 72) link_NAG-ASN : angle 10.37923 / 7.05 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 37 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9527 (ppp) cc_final: 0.9186 (ppp) REVERT: A 107 ASP cc_start: 0.9400 (m-30) cc_final: 0.9183 (m-30) REVERT: A 193 LEU cc_start: 0.9450 (tp) cc_final: 0.9183 (tp) REVERT: A 383 PHE cc_start: 0.9713 (m-80) cc_final: 0.9286 (m-80) REVERT: A 453 LEU cc_start: 0.9613 (tp) cc_final: 0.9344 (tp) REVERT: A 475 MET cc_start: 0.7697 (tpt) cc_final: 0.7141 (tpt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0599 time to fit residues: 3.0042 Evaluate side-chains 29 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.148 Evaluate side-chains 31 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.040 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: D 584 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8583 (mt-10) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0796 time to fit residues: 2.6567 Evaluate side-chains 28 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.049 Evaluate side-chains 25 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.037 Fit side-chains REVERT: I 37 LEU cc_start: 0.8823 (mp) cc_final: 0.8095 (tt) REVERT: I 51 MET cc_start: 0.9515 (ttp) cc_final: 0.8988 (tmm) REVERT: I 72 ASP cc_start: 0.9254 (t70) cc_final: 0.8887 (p0) REVERT: I 100 LEU cc_start: 0.8947 (pt) cc_final: 0.8736 (pp) REVERT: I 100 ASP cc_start: 0.9213 (t0) cc_final: 0.8931 (m-30) REVERT: I 100 TYR cc_start: 0.8745 (p90) cc_final: 0.8348 (p90) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0376 time to fit residues: 1.1036 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 Evaluate side-chains 22 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.032 Fit side-chains REVERT: N 95 PHE cc_start: 0.7930 (t80) cc_final: 0.7675 (p90) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0595 time to fit residues: 1.4375 Evaluate side-chains 12 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 227 optimal weight: 8.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.043720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036961 restraints weight = 455.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.038325 restraints weight = 303.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.038939 restraints weight = 236.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.038939 restraints weight = 201.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.038939 restraints weight = 201.509| |-----------------------------------------------------------------------------| r_work (final): 0.2511 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.050114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.046080 restraints weight = 283.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.046668 restraints weight = 186.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.047239 restraints weight = 138.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.047625 restraints weight = 107.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.047926 restraints weight = 86.201| |-----------------------------------------------------------------------------| r_work (final): 0.2475 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.056909 restraints weight = 716.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057692 restraints weight = 455.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.058214 restraints weight = 310.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058546 restraints weight = 228.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058708 restraints weight = 182.633| |-----------------------------------------------------------------------------| r_work (final): 0.2968 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.047617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035447 restraints weight = 26210.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036931 restraints weight = 16756.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038051 restraints weight = 12087.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.038931 restraints weight = 9359.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039622 restraints weight = 7623.984| |-----------------------------------------------------------------------------| r_work (final): 0.2832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.036038 restraints weight = 9293.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.037338 restraints weight = 5299.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038228 restraints weight = 3615.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.038710 restraints weight = 2744.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039231 restraints weight = 2295.467| |-----------------------------------------------------------------------------| r_work (final): 0.2705 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.033059 restraints weight = 7130.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.034290 restraints weight = 4398.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.035220 restraints weight = 3150.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.035956 restraints weight = 2420.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036485 restraints weight = 1953.627| |-----------------------------------------------------------------------------| r_work (final): 0.2659 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.029823 restraints weight = 5831.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.031237 restraints weight = 3596.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.032345 restraints weight = 2545.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.033197 restraints weight = 1953.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.033829 restraints weight = 1557.246| |-----------------------------------------------------------------------------| r_work (final): 0.2546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.052540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.050489 restraints weight = 658.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051246 restraints weight = 254.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.051778 restraints weight = 132.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.052036 restraints weight = 74.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052191 restraints weight = 44.043| |-----------------------------------------------------------------------------| r_work (final): 0.2831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.046281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.039567 restraints weight = 710.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.039974 restraints weight = 549.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.040026 restraints weight = 475.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.040056 restraints weight = 466.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.040410 restraints weight = 461.802| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.578 22044 Z= 0.729 Angle : 1.976 46.796 30237 Z= 0.768 Chirality : 0.136 2.909 3837 Planarity : 0.007 0.120 3516 Dihedral : 7.529 54.082 2634 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.21 % Favored : 92.66 % Rotamer: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.15), residues: 2412 helix: -0.96 (0.25), residues: 375 sheet: -0.56 (0.19), residues: 651 loop : -2.04 (0.14), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 308 TYR 0.064 0.003 TYR L 30 PHE 0.071 0.003 PHE M 32 TRP 0.028 0.002 TRP J 100 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.34 (21831) covalent geometry : angle 1.51942 / 0.64 (29631) SS BOND : bond 0.06718 / 4.56 ( 33) SS BOND : angle 3.01617 / 2.19 ( 66) hydrogen bonds : bond 0.05526 / 3.56 ( 726) hydrogen bonds : angle 6.80318 / 4.86 ( 1977) link_ALPHA1-3 : bond 0.23800 / 13.88 ( 12) link_ALPHA1-3 : angle 11.51686 / 6.27 ( 36) link_ALPHA1-6 : bond 0.41797 / 24.87 ( 15) link_ALPHA1-6 : angle 20.91604 / 13.39 ( 45) link_BETA1-4 : bond 0.00853 / 0.52 ( 81) link_BETA1-4 : angle 2.43614 / 1.71 ( 243) link_NAG-ASN : bond 0.05443 / 3.40 ( 72) link_NAG-ASN : angle 10.34461 / 7.05 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 35 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9551 (ppp) cc_final: 0.9213 (ppp) REVERT: A 129 LEU cc_start: 0.9417 (tp) cc_final: 0.9206 (tp) REVERT: A 193 LEU cc_start: 0.9444 (tp) cc_final: 0.9196 (tp) REVERT: A 383 PHE cc_start: 0.9706 (m-80) cc_final: 0.9283 (m-80) REVERT: A 453 LEU cc_start: 0.9588 (tp) cc_final: 0.9328 (tp) REVERT: A 475 MET cc_start: 0.7916 (tpt) cc_final: 0.7583 (tpt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0446 time to fit residues: 2.3096 Evaluate side-chains 28 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.144 Evaluate side-chains 28 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8527 (mt-10) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0865 time to fit residues: 2.6000 Evaluate side-chains 25 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.047 Evaluate side-chains 23 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.046 Fit side-chains REVERT: I 34 MET cc_start: 0.9309 (mmp) cc_final: 0.9102 (mmm) REVERT: I 37 LEU cc_start: 0.8833 (mp) cc_final: 0.8034 (tt) REVERT: I 51 MET cc_start: 0.9551 (ttp) cc_final: 0.9009 (tmm) REVERT: I 72 ASP cc_start: 0.9262 (t70) cc_final: 0.8882 (p0) REVERT: I 100 ASP cc_start: 0.8933 (t0) cc_final: 0.8629 (m-30) REVERT: I 100 TYR cc_start: 0.8803 (p90) cc_final: 0.8251 (p90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0307 time to fit residues: 0.8700 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.037 Evaluate side-chains 20 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: N 48 MET cc_start: 0.6574 (mmm) cc_final: 0.5557 (tpp) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0377 time to fit residues: 0.8770 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 73 optimal weight: 0.0030 chunk 58 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 18 optimal weight: 0.0020 chunk 129 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 425 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.037410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.037347 restraints weight = 506.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037379 restraints weight = 32.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037394 restraints weight = 5.170 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037394 restraints weight = 2.480 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037394 restraints weight = 2.480 | |-----------------------------------------------------------------------------| r_work (final): 0.2535 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.049892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.046203 restraints weight = 271.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.046848 restraints weight = 177.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.047315 restraints weight = 129.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.047692 restraints weight = 98.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.048040 restraints weight = 77.916| |-----------------------------------------------------------------------------| r_work (final): 0.2467 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057579 restraints weight = 751.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058417 restraints weight = 432.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058901 restraints weight = 296.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059203 restraints weight = 228.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059477 restraints weight = 194.391| |-----------------------------------------------------------------------------| r_work (final): 0.2974 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035834 restraints weight = 24414.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037406 restraints weight = 15658.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.038588 restraints weight = 11254.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039507 restraints weight = 8663.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.040150 restraints weight = 7028.599| |-----------------------------------------------------------------------------| r_work (final): 0.2859 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.036537 restraints weight = 9566.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037847 restraints weight = 5303.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038749 restraints weight = 3573.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.039387 restraints weight = 2699.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.039821 restraints weight = 2196.731| |-----------------------------------------------------------------------------| r_work (final): 0.2725 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032619 restraints weight = 7016.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.034023 restraints weight = 4184.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.034974 restraints weight = 2904.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.035849 restraints weight = 2189.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036463 restraints weight = 1762.080| |-----------------------------------------------------------------------------| r_work (final): 0.2712 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.039171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.030533 restraints weight = 5518.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.032014 restraints weight = 3256.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.033041 restraints weight = 2244.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.033947 restraints weight = 1703.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.034614 restraints weight = 1329.467| |-----------------------------------------------------------------------------| r_work (final): 0.2554 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.051411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.048801 restraints weight = 633.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.049599 restraints weight = 311.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.050122 restraints weight = 186.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.050471 restraints weight = 122.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.050732 restraints weight = 84.109| |-----------------------------------------------------------------------------| r_work (final): 0.2775 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.044493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.037509 restraints weight = 716.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.037932 restraints weight = 545.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.038132 restraints weight = 473.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.038433 restraints weight = 434.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.038512 restraints weight = 408.087| |-----------------------------------------------------------------------------| r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.571 22044 Z= 0.696 Angle : 1.890 46.700 30237 Z= 0.731 Chirality : 0.133 2.734 3837 Planarity : 0.006 0.066 3516 Dihedral : 7.388 54.450 2634 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 0.28 % Allowed : 2.83 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.15), residues: 2412 helix: -0.95 (0.25), residues: 375 sheet: -0.38 (0.19), residues: 633 loop : -1.99 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 308 TYR 0.034 0.002 TYR I 100A PHE 0.036 0.003 PHE M 32 TRP 0.051 0.003 TRP C 427 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (21831) covalent geometry : angle 1.42343 / 0.60 (29631) SS BOND : bond 0.06633 / 4.46 ( 33) SS BOND : angle 2.25709 / 1.62 ( 66) hydrogen bonds : bond 0.04834 / 3.16 ( 726) hydrogen bonds : angle 6.66262 / 4.74 ( 1977) link_ALPHA1-3 : bond 0.23800 / 13.88 ( 12) link_ALPHA1-3 : angle 11.35530 / 6.11 ( 36) link_ALPHA1-6 : bond 0.41395 / 24.62 ( 15) link_ALPHA1-6 : angle 20.94583 / 13.35 ( 45) link_BETA1-4 : bond 0.00817 / 0.50 ( 81) link_BETA1-4 : angle 2.23623 / 1.57 ( 243) link_NAG-ASN : bond 0.05430 / 3.36 ( 72) link_NAG-ASN : angle 10.11317 / 6.88 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 37 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9539 (ppp) cc_final: 0.9171 (ppp) REVERT: A 193 LEU cc_start: 0.9464 (tp) cc_final: 0.9210 (tp) REVERT: A 383 PHE cc_start: 0.9666 (m-80) cc_final: 0.9259 (m-80) REVERT: A 453 LEU cc_start: 0.9603 (tp) cc_final: 0.9327 (tp) REVERT: A 475 MET cc_start: 0.8358 (tpt) cc_final: 0.7886 (tpp) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0421 time to fit residues: 2.3101 Evaluate side-chains 30 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.143 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8177 (mtm) cc_final: 0.7914 (ptp) REVERT: B 584 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 587 LEU cc_start: 0.9882 (mm) cc_final: 0.9625 (pp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0779 time to fit residues: 2.5211 Evaluate side-chains 24 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.037 Evaluate side-chains 25 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 Fit side-chains REVERT: I 34 MET cc_start: 0.9280 (mmp) cc_final: 0.9057 (mmm) REVERT: I 37 LEU cc_start: 0.8774 (mp) cc_final: 0.7989 (tt) REVERT: I 51 MET cc_start: 0.9541 (ttp) cc_final: 0.8982 (tmm) REVERT: I 72 ASP cc_start: 0.9251 (t70) cc_final: 0.8874 (p0) REVERT: I 100 ASP cc_start: 0.8949 (t0) cc_final: 0.8614 (m-30) REVERT: I 100 TYR cc_start: 0.8783 (p90) cc_final: 0.8262 (p90) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0287 time to fit residues: 0.8788 Evaluate side-chains 20 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.039 Evaluate side-chains 19 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: N 30 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: N 48 MET cc_start: 0.6678 (mmm) cc_final: 0.5664 (tpp) REVERT: N 88 CYS cc_start: 0.5937 (t) cc_final: 0.5195 (t) REVERT: N 103 LYS cc_start: 0.9687 (tptp) cc_final: 0.9481 (tptt) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.0494 time to fit residues: 1.0530 Evaluate side-chains 12 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 221 optimal weight: 4.9990 chunk 118 optimal weight: 0.0050 chunk 161 optimal weight: 0.0970 chunk 63 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 425 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.037215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037151 restraints weight = 599.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037189 restraints weight = 34.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037183 restraints weight = 3.541 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037182 restraints weight = 0.379 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037182 restraints weight = 0.291 | |-----------------------------------------------------------------------------| r_work (final): 0.2544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.050309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.046995 restraints weight = 249.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.047609 restraints weight = 166.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.048064 restraints weight = 120.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.048476 restraints weight = 90.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.048783 restraints weight = 69.525| |-----------------------------------------------------------------------------| r_work (final): 0.2495 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057647 restraints weight = 755.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058452 restraints weight = 475.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058955 restraints weight = 339.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059376 restraints weight = 271.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059662 restraints weight = 219.567| |-----------------------------------------------------------------------------| r_work (final): 0.3011 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035860 restraints weight = 23563.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037385 restraints weight = 15325.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.038584 restraints weight = 11159.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039478 restraints weight = 8693.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.040057 restraints weight = 7111.828| |-----------------------------------------------------------------------------| r_work (final): 0.2862 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.036128 restraints weight = 9746.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037378 restraints weight = 5357.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038231 restraints weight = 3634.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.038855 restraints weight = 2739.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.039299 restraints weight = 2225.052| |-----------------------------------------------------------------------------| r_work (final): 0.2711 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032199 restraints weight = 6568.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.033549 restraints weight = 3921.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.034489 restraints weight = 2776.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.035098 restraints weight = 2134.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.035699 restraints weight = 1774.885| |-----------------------------------------------------------------------------| r_work (final): 0.2678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.039930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.031570 restraints weight = 5579.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.033172 restraints weight = 3046.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034380 restraints weight = 2053.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.035300 restraints weight = 1479.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.035872 restraints weight = 1125.434| |-----------------------------------------------------------------------------| r_work (final): 0.2655 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.051554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.049778 restraints weight = 733.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.050118 restraints weight = 451.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.050423 restraints weight = 331.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.050670 restraints weight = 254.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.050669 restraints weight = 187.174| |-----------------------------------------------------------------------------| r_work (final): 0.2710 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.043798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.036943 restraints weight = 686.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.037216 restraints weight = 536.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.037440 restraints weight = 476.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.037440 restraints weight = 445.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.037440 restraints weight = 445.689| |-----------------------------------------------------------------------------| r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.566 22044 Z= 0.690 Angle : 1.884 46.501 30237 Z= 0.730 Chirality : 0.131 2.590 3837 Planarity : 0.005 0.056 3516 Dihedral : 7.360 54.460 2634 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.16), residues: 2412 helix: -0.87 (0.25), residues: 372 sheet: -0.12 (0.20), residues: 627 loop : -2.02 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 192 TYR 0.108 0.003 TYR L 30 PHE 0.027 0.002 PHE L 95B TRP 0.025 0.002 TRP J 100 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 (21831) covalent geometry : angle 1.41890 / 0.60 (29631) SS BOND : bond 0.06449 / 4.34 ( 33) SS BOND : angle 2.24876 / 1.64 ( 66) hydrogen bonds : bond 0.04731 / 3.07 ( 726) hydrogen bonds : angle 6.63309 / 4.73 ( 1977) link_ALPHA1-3 : bond 0.23833 / 13.90 ( 12) link_ALPHA1-3 : angle 11.23973 / 6.03 ( 36) link_ALPHA1-6 : bond 0.41078 / 24.43 ( 15) link_ALPHA1-6 : angle 20.96522 / 13.33 ( 45) link_BETA1-4 : bond 0.00752 / 0.47 ( 81) link_BETA1-4 : angle 2.17092 / 1.53 ( 243) link_NAG-ASN : bond 0.05403 / 3.34 ( 72) link_NAG-ASN : angle 10.05039 / 6.84 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.9566 (ppp) cc_final: 0.9262 (ppp) REVERT: E 193 LEU cc_start: 0.9574 (tp) cc_final: 0.9351 (tp) REVERT: E 259 LEU cc_start: 0.9469 (mm) cc_final: 0.8774 (tp) REVERT: E 383 PHE cc_start: 0.9659 (m-80) cc_final: 0.9179 (m-80) REVERT: E 426 MET cc_start: 0.7853 (ttp) cc_final: 0.7273 (ttp) REVERT: E 453 LEU cc_start: 0.9581 (tp) cc_final: 0.9117 (tp) REVERT: E 475 MET cc_start: 0.8185 (tpt) cc_final: 0.7622 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0584 time to fit residues: 3.7430 Evaluate side-chains 34 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.147 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8474 (mt-10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0813 time to fit residues: 2.6277 Evaluate side-chains 24 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.039 Evaluate side-chains 24 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.040 Fit side-chains REVERT: I 34 MET cc_start: 0.9315 (mmp) cc_final: 0.9056 (mmm) REVERT: I 37 LEU cc_start: 0.8753 (mp) cc_final: 0.8067 (tt) REVERT: I 51 MET cc_start: 0.9559 (ttp) cc_final: 0.8998 (tmm) REVERT: I 72 ASP cc_start: 0.9239 (t70) cc_final: 0.8849 (p0) REVERT: I 100 ASP cc_start: 0.8927 (t0) cc_final: 0.8650 (m-30) REVERT: I 100 TYR cc_start: 0.8832 (p90) cc_final: 0.8241 (p90) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0300 time to fit residues: 0.8785 Evaluate side-chains 20 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.039 Evaluate side-chains 18 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: N 48 MET cc_start: 0.6797 (mmm) cc_final: 0.5629 (tpp) REVERT: N 104 LEU cc_start: 0.9777 (tp) cc_final: 0.9574 (tp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0390 time to fit residues: 0.8096 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 137 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN N 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037090 restraints weight = 683.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037105 restraints weight = 34.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037117 restraints weight = 3.511 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037117 restraints weight = 0.374 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037117 restraints weight = 0.373 | |-----------------------------------------------------------------------------| r_work (final): 0.2537 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.049753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.046690 restraints weight = 230.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.047295 restraints weight = 154.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.047735 restraints weight = 110.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.048141 restraints weight = 82.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.048476 restraints weight = 61.914| |-----------------------------------------------------------------------------| r_work (final): 0.2474 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.057701 restraints weight = 706.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058474 restraints weight = 440.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.059069 restraints weight = 318.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059345 restraints weight = 248.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059706 restraints weight = 212.522| |-----------------------------------------------------------------------------| r_work (final): 0.3016 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.036656 restraints weight = 25835.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038242 restraints weight = 16462.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.039551 restraints weight = 11744.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040466 restraints weight = 9019.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041209 restraints weight = 7324.276| |-----------------------------------------------------------------------------| r_work (final): 0.2881 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.041769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.033026 restraints weight = 7896.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.034311 restraints weight = 4720.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.035213 restraints weight = 3280.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.035851 restraints weight = 2498.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.036297 restraints weight = 2044.702| |-----------------------------------------------------------------------------| r_work (final): 0.2643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.040645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.031653 restraints weight = 7147.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.032859 restraints weight = 4229.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033770 restraints weight = 2989.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.034622 restraints weight = 2302.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.035184 restraints weight = 1841.570| |-----------------------------------------------------------------------------| r_work (final): 0.2671 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.040955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.033042 restraints weight = 5485.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.034497 restraints weight = 2967.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.035723 restraints weight = 1989.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.036409 restraints weight = 1437.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.036971 restraints weight = 1104.215| |-----------------------------------------------------------------------------| r_work (final): 0.2660 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.053275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.050491 restraints weight = 643.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051198 restraints weight = 359.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051761 restraints weight = 237.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.052123 restraints weight = 160.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052431 restraints weight = 112.052| |-----------------------------------------------------------------------------| r_work (final): 0.2805 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.044720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.038056 restraints weight = 894.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.038202 restraints weight = 716.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.038387 restraints weight = 658.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.038583 restraints weight = 609.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.038699 restraints weight = 582.173| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.562 22044 Z= 0.682 Angle : 1.864 46.333 30237 Z= 0.714 Chirality : 0.129 2.485 3837 Planarity : 0.005 0.056 3516 Dihedral : 7.355 54.348 2634 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2412 helix: -0.90 (0.26), residues: 375 sheet: -0.22 (0.20), residues: 642 loop : -1.94 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 585 TYR 0.036 0.002 TYR H 100A PHE 0.024 0.003 PHE L 95B TRP 0.023 0.002 TRP B 571 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (21831) covalent geometry : angle 1.39310 / 0.58 (29631) SS BOND : bond 0.06426 / 4.33 ( 33) SS BOND : angle 2.82734 / 1.99 ( 66) hydrogen bonds : bond 0.04514 / 2.94 ( 726) hydrogen bonds : angle 6.58015 / 4.69 ( 1977) link_ALPHA1-3 : bond 0.23818 / 13.89 ( 12) link_ALPHA1-3 : angle 11.20549 / 5.98 ( 36) link_ALPHA1-6 : bond 0.40780 / 24.26 ( 15) link_ALPHA1-6 : angle 20.98840 / 13.32 ( 45) link_BETA1-4 : bond 0.00731 / 0.46 ( 81) link_BETA1-4 : angle 2.19292 / 1.52 ( 243) link_NAG-ASN : bond 0.05429 / 3.35 ( 72) link_NAG-ASN : angle 9.97966 / 6.80 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 36 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9524 (ppp) cc_final: 0.9110 (ppp) REVERT: A 108 VAL cc_start: 0.9717 (p) cc_final: 0.9510 (p) REVERT: A 193 LEU cc_start: 0.9448 (tp) cc_final: 0.9172 (tp) REVERT: A 383 PHE cc_start: 0.9602 (m-80) cc_final: 0.9181 (m-80) REVERT: A 426 MET cc_start: 0.7055 (ttp) cc_final: 0.6433 (ttp) REVERT: A 453 LEU cc_start: 0.9576 (tp) cc_final: 0.9278 (tp) REVERT: A 475 MET cc_start: 0.8243 (tpt) cc_final: 0.7560 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0428 time to fit residues: 2.2547 Evaluate side-chains 28 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.119 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8459 (mt-10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0798 time to fit residues: 2.4775 Evaluate side-chains 23 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.038 Evaluate side-chains 23 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.039 Fit side-chains REVERT: I 34 MET cc_start: 0.9303 (mmp) cc_final: 0.9058 (mmm) REVERT: I 37 LEU cc_start: 0.8838 (mp) cc_final: 0.7962 (tt) REVERT: I 51 MET cc_start: 0.9571 (ttp) cc_final: 0.9014 (tmm) REVERT: I 72 ASP cc_start: 0.9235 (t70) cc_final: 0.8847 (p0) REVERT: I 100 ASP cc_start: 0.8877 (t0) cc_final: 0.8315 (t70) REVERT: I 100 TYR cc_start: 0.8762 (p90) cc_final: 0.8338 (p90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0278 time to fit residues: 0.7959 Evaluate side-chains 19 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.037 Evaluate side-chains 17 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: N 48 MET cc_start: 0.6813 (mmm) cc_final: 0.5791 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0405 time to fit residues: 0.8014 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.036013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.035919 restraints weight = 639.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.035983 restraints weight = 58.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.035986 restraints weight = 11.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.035991 restraints weight = 2.979 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.035991 restraints weight = 0.897 | |-----------------------------------------------------------------------------| r_work (final): 0.2470 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.048744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.045825 restraints weight = 269.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.046418 restraints weight = 175.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.046914 restraints weight = 122.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.047364 restraints weight = 87.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.047729 restraints weight = 62.890| |-----------------------------------------------------------------------------| r_work (final): 0.2457 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058768 restraints weight = 762.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059515 restraints weight = 460.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060155 restraints weight = 329.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060557 restraints weight = 251.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060557 restraints weight = 205.295| |-----------------------------------------------------------------------------| r_work (final): 0.3036 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.036348 restraints weight = 25404.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.037986 restraints weight = 16265.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.039230 restraints weight = 11670.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040188 restraints weight = 8990.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040887 restraints weight = 7308.703| |-----------------------------------------------------------------------------| r_work (final): 0.2882 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.042408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.033968 restraints weight = 8633.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.035298 restraints weight = 5029.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.036219 restraints weight = 3446.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.036887 restraints weight = 2625.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.037328 restraints weight = 2131.439| |-----------------------------------------------------------------------------| r_work (final): 0.2647 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.036570 restraints weight = 7043.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.037955 restraints weight = 4513.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038934 restraints weight = 3212.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.039607 restraints weight = 2463.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.040269 restraints weight = 2021.536| |-----------------------------------------------------------------------------| r_work (final): 0.2822 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.042190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.034570 restraints weight = 5276.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.036201 restraints weight = 2724.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.037305 restraints weight = 1742.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.038161 restraints weight = 1252.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038805 restraints weight = 958.568| |-----------------------------------------------------------------------------| r_work (final): 0.2714 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.051475 restraints weight = 823.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.051906 restraints weight = 526.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.052200 restraints weight = 346.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.052416 restraints weight = 239.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.052523 restraints weight = 161.039| |-----------------------------------------------------------------------------| r_work (final): 0.2770 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.042981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.038573 restraints weight = 646.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.039236 restraints weight = 342.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.039732 restraints weight = 247.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.040205 restraints weight = 196.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.040506 restraints weight = 160.595| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.558 22044 Z= 0.670 Angle : 1.832 46.102 30237 Z= 0.701 Chirality : 0.128 2.426 3837 Planarity : 0.005 0.055 3516 Dihedral : 7.320 54.035 2634 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2412 helix: -0.77 (0.26), residues: 378 sheet: -0.21 (0.20), residues: 642 loop : -1.91 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 308 TYR 0.038 0.002 TYR M 30 PHE 0.027 0.002 PHE I 67 TRP 0.037 0.003 TRP F 571 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 (21831) covalent geometry : angle 1.35672 / 0.57 (29631) SS BOND : bond 0.06172 / 4.12 ( 33) SS BOND : angle 2.16312 / 1.56 ( 66) hydrogen bonds : bond 0.04336 / 2.85 ( 726) hydrogen bonds : angle 6.53715 / 4.66 ( 1977) link_ALPHA1-3 : bond 0.23836 / 13.90 ( 12) link_ALPHA1-3 : angle 11.16654 / 5.94 ( 36) link_ALPHA1-6 : bond 0.40523 / 24.10 ( 15) link_ALPHA1-6 : angle 21.02200 / 13.31 ( 45) link_BETA1-4 : bond 0.00742 / 0.47 ( 81) link_BETA1-4 : angle 2.05712 / 1.43 ( 243) link_NAG-ASN : bond 0.05492 / 3.39 ( 72) link_NAG-ASN : angle 9.92207 / 6.78 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 41 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.9547 (ppp) cc_final: 0.9259 (ppp) REVERT: E 193 LEU cc_start: 0.9563 (tp) cc_final: 0.9358 (tp) REVERT: E 383 PHE cc_start: 0.9602 (m-80) cc_final: 0.9207 (m-80) REVERT: E 426 MET cc_start: 0.7720 (ttp) cc_final: 0.7040 (ttp) REVERT: E 453 LEU cc_start: 0.9572 (tp) cc_final: 0.9118 (tp) REVERT: E 475 MET cc_start: 0.8166 (tpt) cc_final: 0.7593 (tpp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0473 time to fit residues: 2.7831 Evaluate side-chains 31 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.145 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 587 LEU cc_start: 0.9861 (mm) cc_final: 0.9591 (pp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0807 time to fit residues: 2.6006 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.040 Evaluate side-chains 22 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.037 Fit side-chains REVERT: H 34 MET cc_start: 0.9393 (mmp) cc_final: 0.8923 (mmm) REVERT: H 37 LEU cc_start: 0.8464 (mp) cc_final: 0.7587 (tt) REVERT: H 51 MET cc_start: 0.9553 (ttp) cc_final: 0.8965 (tmm) REVERT: H 72 ASP cc_start: 0.9167 (t70) cc_final: 0.8687 (p0) REVERT: H 100 ASP cc_start: 0.8817 (t0) cc_final: 0.8526 (m-30) REVERT: H 100 TYR cc_start: 0.8806 (p90) cc_final: 0.8068 (p90) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0275 time to fit residues: 0.7550 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.038 Evaluate side-chains 20 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: M 75 ILE cc_start: 0.9719 (mm) cc_final: 0.9286 (mm) REVERT: M 95 PHE cc_start: 0.9016 (m-10) cc_final: 0.8790 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0382 time to fit residues: 0.8850 Evaluate side-chains 12 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 116 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 215 optimal weight: 0.3980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.036653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.036599 restraints weight = 579.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.036619 restraints weight = 46.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.036613 restraints weight = 7.077 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.036616 restraints weight = 1.104 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.036615 restraints weight = 0.541 | |-----------------------------------------------------------------------------| r_work (final): 0.2474 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.049056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.046082 restraints weight = 263.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.046714 restraints weight = 167.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.047202 restraints weight = 115.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.047688 restraints weight = 81.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.048044 restraints weight = 57.733| |-----------------------------------------------------------------------------| r_work (final): 0.2445 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059240 restraints weight = 734.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059904 restraints weight = 433.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060519 restraints weight = 315.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060948 restraints weight = 243.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.061088 restraints weight = 200.796| |-----------------------------------------------------------------------------| r_work (final): 0.3033 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.036505 restraints weight = 25303.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038078 restraints weight = 16411.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.039297 restraints weight = 11922.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.040219 restraints weight = 9305.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040950 restraints weight = 7612.514| |-----------------------------------------------------------------------------| r_work (final): 0.2878 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.041578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.032572 restraints weight = 8044.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.033809 restraints weight = 4889.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.034712 restraints weight = 3445.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.035370 restraints weight = 2658.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.035766 restraints weight = 2183.257| |-----------------------------------------------------------------------------| r_work (final): 0.2638 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.032359 restraints weight = 6996.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033830 restraints weight = 4345.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.034919 restraints weight = 3096.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.035765 restraints weight = 2378.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.036389 restraints weight = 1939.568| |-----------------------------------------------------------------------------| r_work (final): 0.2702 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.032688 restraints weight = 5450.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034457 restraints weight = 2979.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.035694 restraints weight = 1985.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.036624 restraints weight = 1462.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.037372 restraints weight = 1149.033| |-----------------------------------------------------------------------------| r_work (final): 0.2684 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.050731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.049318 restraints weight = 911.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.049860 restraints weight = 509.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050216 restraints weight = 296.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.050418 restraints weight = 157.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.050492 restraints weight = 85.476| |-----------------------------------------------------------------------------| r_work (final): 0.2732 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.041543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.034797 restraints weight = 884.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.035028 restraints weight = 660.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.035385 restraints weight = 579.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.035385 restraints weight = 509.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.035385 restraints weight = 509.613| |-----------------------------------------------------------------------------| r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.555 22044 Z= 0.669 Angle : 1.810 45.921 30237 Z= 0.692 Chirality : 0.128 2.422 3837 Planarity : 0.005 0.055 3516 Dihedral : 7.276 53.753 2634 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.16), residues: 2412 helix: -0.79 (0.26), residues: 378 sheet: -0.22 (0.20), residues: 642 loop : -1.86 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 588 TYR 0.024 0.002 TYR L 30 PHE 0.018 0.002 PHE M 95B TRP 0.036 0.002 TRP F 571 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (21831) covalent geometry : angle 1.33791 / 0.56 (29631) SS BOND : bond 0.06034 / 3.99 ( 33) SS BOND : angle 2.44465 / 1.80 ( 66) hydrogen bonds : bond 0.04343 / 2.87 ( 726) hydrogen bonds : angle 6.56745 / 4.69 ( 1977) link_ALPHA1-3 : bond 0.23851 / 13.91 ( 12) link_ALPHA1-3 : angle 11.08133 / 5.87 ( 36) link_ALPHA1-6 : bond 0.40323 / 23.98 ( 15) link_ALPHA1-6 : angle 21.05386 / 13.32 ( 45) link_BETA1-4 : bond 0.00592 / 0.37 ( 81) link_BETA1-4 : angle 2.03285 / 1.41 ( 243) link_NAG-ASN : bond 0.05414 / 3.33 ( 72) link_NAG-ASN : angle 9.68434 / 6.58 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 41 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.9569 (ppp) cc_final: 0.9267 (ppp) REVERT: E 193 LEU cc_start: 0.9565 (tp) cc_final: 0.9364 (tp) REVERT: E 383 PHE cc_start: 0.9596 (m-80) cc_final: 0.9203 (m-80) REVERT: E 426 MET cc_start: 0.7532 (ttp) cc_final: 0.6925 (ttp) REVERT: E 453 LEU cc_start: 0.9567 (tp) cc_final: 0.9110 (tp) REVERT: E 475 MET cc_start: 0.8170 (tpt) cc_final: 0.7593 (tpp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0403 time to fit residues: 2.4561 Evaluate side-chains 30 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.156 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 587 LEU cc_start: 0.9880 (mm) cc_final: 0.9643 (pp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0792 time to fit residues: 2.4738 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.041 Evaluate side-chains 19 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.040 Fit side-chains REVERT: I 34 MET cc_start: 0.9289 (mmp) cc_final: 0.8982 (mmm) REVERT: I 37 LEU cc_start: 0.8641 (mp) cc_final: 0.7897 (tt) REVERT: I 51 MET cc_start: 0.9580 (ttp) cc_final: 0.9001 (tmm) REVERT: I 72 ASP cc_start: 0.9246 (t70) cc_final: 0.8849 (p0) REVERT: I 100 ASP cc_start: 0.8799 (t0) cc_final: 0.8328 (t0) REVERT: I 100 TYR cc_start: 0.8783 (p90) cc_final: 0.8434 (p90) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0285 time to fit residues: 0.6795 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.038 Evaluate side-chains 17 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.035 Fit side-chains REVERT: M 48 MET cc_start: 0.7343 (tpt) cc_final: 0.6621 (tpt) REVERT: M 75 ILE cc_start: 0.9729 (mm) cc_final: 0.9288 (mm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0248 time to fit residues: 0.5323 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 129 optimal weight: 0.0370 chunk 163 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.038404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.038333 restraints weight = 561.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.038377 restraints weight = 28.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.038383 restraints weight = 3.271 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.038383 restraints weight = 0.779 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.038383 restraints weight = 0.778 | |-----------------------------------------------------------------------------| r_work (final): 0.2609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.049293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.046755 restraints weight = 231.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.047392 restraints weight = 141.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.047954 restraints weight = 91.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.048517 restraints weight = 60.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.048823 restraints weight = 32.566| |-----------------------------------------------------------------------------| r_work (final): 0.2498 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.063844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057363 restraints weight = 852.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058734 restraints weight = 551.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059925 restraints weight = 398.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060491 restraints weight = 287.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.061294 restraints weight = 225.619| |-----------------------------------------------------------------------------| r_work (final): 0.3062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035955 restraints weight = 25732.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.037529 restraints weight = 16747.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038682 restraints weight = 12152.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039619 restraints weight = 9540.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.040350 restraints weight = 7793.052| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.042812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.034471 restraints weight = 8788.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.035792 restraints weight = 5178.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.036739 restraints weight = 3594.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.037413 restraints weight = 2733.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.037871 restraints weight = 2219.289| |-----------------------------------------------------------------------------| r_work (final): 0.2667 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032411 restraints weight = 6896.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.033790 restraints weight = 4342.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.034853 restraints weight = 3099.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035639 restraints weight = 2391.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.036261 restraints weight = 1944.642| |-----------------------------------------------------------------------------| r_work (final): 0.2695 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.040799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.032395 restraints weight = 5577.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.033940 restraints weight = 3137.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.035203 restraints weight = 2129.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.036167 restraints weight = 1560.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036843 restraints weight = 1186.985| |-----------------------------------------------------------------------------| r_work (final): 0.2681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.085480 restraints weight = 625.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086149 restraints weight = 482.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.086725 restraints weight = 397.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087198 restraints weight = 331.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087579 restraints weight = 286.279| |-----------------------------------------------------------------------------| r_work (final): 0.3028 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.042218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.035512 restraints weight = 827.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.035889 restraints weight = 643.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.036058 restraints weight = 563.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.036234 restraints weight = 523.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.036234 restraints weight = 491.044| |-----------------------------------------------------------------------------| r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.553 22044 Z= 0.665 Angle : 1.805 45.809 30237 Z= 0.686 Chirality : 0.126 2.337 3837 Planarity : 0.005 0.054 3516 Dihedral : 7.226 53.454 2634 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2412 helix: -0.82 (0.26), residues: 378 sheet: -0.21 (0.20), residues: 642 loop : -1.81 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100E TYR 0.031 0.002 TYR N 30 PHE 0.016 0.002 PHE L 95B TRP 0.035 0.002 TRP F 571 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (21831) covalent geometry : angle 1.33333 / 0.55 (29631) SS BOND : bond 0.05797 / 3.80 ( 33) SS BOND : angle 1.95775 / 1.41 ( 66) hydrogen bonds : bond 0.04216 / 2.78 ( 726) hydrogen bonds : angle 6.48932 / 4.62 ( 1977) link_ALPHA1-3 : bond 0.23862 / 13.92 ( 12) link_ALPHA1-3 : angle 11.04897 / 5.85 ( 36) link_ALPHA1-6 : bond 0.40191 / 23.91 ( 15) link_ALPHA1-6 : angle 21.07090 / 13.32 ( 45) link_BETA1-4 : bond 0.00681 / 0.43 ( 81) link_BETA1-4 : angle 2.00268 / 1.40 ( 243) link_NAG-ASN : bond 0.05439 / 3.34 ( 72) link_NAG-ASN : angle 9.66951 / 6.55 ( 216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.34 seconds wall clock time: 48 minutes 1.41 seconds (2881.41 seconds total)