Starting phenix.real_space_refine on Sun Sep 13 06:31:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.cif" model { file = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mn7_9166/09_2026/6mn7_9166.cif" } resolution = 4.8 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= 0.011 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 135 5.16 5 C 13365 2.51 5 N 3411 2.21 5 O 4536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 21447 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "H" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "I" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: 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: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 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: "j" 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: "k" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: "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: 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: "z" 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: "0" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" 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: "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: 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.42, per 1000 atoms: 0.25 Number of scatterers: 21447 At special positions: 0 Unit cell: (156.2, 156.2, 140.8, 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 135 16.00 O 4536 8.00 N 3411 7.00 C 13365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.10 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=1.62 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=2.11 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.09 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.22 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.10 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.11 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.11 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=1.62 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=2.11 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.09 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.22 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.10 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.11 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.11 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=1.62 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.11 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.09 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.22 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 215 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 215 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 215 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM20254 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19481 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20999 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20254 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19481 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20999 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19337 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20855 O5 NAG y 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20110 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20677 O5 NAG u 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19159 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19932 O5 NAG e 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19187 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19960 O5 NAG f 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20705 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN 0 8 " - " MAN 0 9 " " MAN P 4 " - " MAN P 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN g 4 " - " MAN g 5 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN k 8 " - " MAN k 9 " " MAN w 4 " - " MAN w 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 10 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 10 " " BMA w 3 " - " MAN w 4 " " MAN w 6 " - " MAN w 7 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 7 " " MAN z 4 " - " MAN z 5 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " MAN 0 7 " - " MAN 0 8 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA g 3 " - " MAN g 6 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 8 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMA z 3 " - " MAN z 4 " " MAN z 4 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " 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 m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG 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 D 332 " " NAG 1 1 " - " ASN D 355 " " NAG 2 1 " - " ASN D 363 " " NAG 3 1 " - " ASN D 386 " " NAG 4 1 " - " ASN D 392 " " NAG 5 1 " - " ASN D 448 " " NAG 6 1 " - " ASN E 611 " " NAG 7 1 " - " ASN F 611 " " NAG A 648 " - " ASN A 339 " " NAG B 703 " - " ASN B 618 " " NAG B 704 " - " ASN B 637 " " NAG C 648 " - " ASN C 339 " " NAG D 648 " - " ASN D 339 " " NAG E 703 " - " ASN E 618 " " NAG E 704 " - " ASN E 637 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 133 " " NAG L 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 355 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN B 611 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 276 " " NAG i 1 " - " ASN C 295 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 363 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 88 " " NAG r 1 " - " ASN D 133 " " NAG s 1 " - " ASN D 156 " " NAG t 1 " - " ASN D 160 " " NAG u 1 " - " ASN D 197 " " NAG v 1 " - " ASN D 234 " " NAG w 1 " - " ASN D 262 " " NAG x 1 " - " ASN D 276 " " NAG y 1 " - " ASN D 295 " " NAG z 1 " - " ASN D 301 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 821.1 milliseconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 20.5% alpha, 32.6% 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 99 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.678A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.271A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.060A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.726A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.979A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.678A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.679A pdb=" N GLN D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 546 removed outlier: 4.060A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.727A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 648 removed outlier: 3.978A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 654 Processing helix chain 'E' and resid 656 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 546 removed outlier: 4.058A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.728A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.979A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 654 Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.557A pdb=" N PHE G 210 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 206 through 210 removed outlier: 3.555A pdb=" N PHE H 210 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 206 through 210 removed outlier: 3.556A pdb=" N PHE I 210 " --> pdb=" O SER I 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 161 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.481A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.818A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.295A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.045A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.819A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.296A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'D' and resid 92 through 94 Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AC8, first strand: chain 'D' and resid 154 through 161 Processing sheet with id=AC9, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.482A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.819A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.295A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.481A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD7, first strand: chain 'G' and resid 132 through 134 Processing sheet with id=AD8, first strand: chain 'G' and resid 137 through 140 removed outlier: 6.367A pdb=" N PHE G 160 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR G 176 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP G 162 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 137 through 140 Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.482A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AE4, first strand: chain 'H' and resid 132 through 134 Processing sheet with id=AE5, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.366A pdb=" N PHE H 160 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR H 176 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 162 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 137 through 140 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.481A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'I' and resid 132 through 134 Processing sheet with id=AF2, first strand: chain 'I' and resid 137 through 140 removed outlier: 6.366A pdb=" N PHE I 160 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR I 176 " --> pdb=" O PHE I 160 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP I 162 " --> pdb=" O LEU I 174 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 137 through 140 750 hydrogen bonds defined for protein. 1872 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: 4.41 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3466 1.32 - 1.45: 6813 1.45 - 1.57: 11367 1.57 - 1.70: 29 1.70 - 1.83: 201 Bond restraints: 21876 Sorted by residual: bond pdb=" CA GLU G 128 " pdb=" C GLU G 128 " ideal model delta sigma weight residual 1.523 1.832 -0.309 1.34e-02 5.57e+03 5.31e+02 bond pdb=" CA GLU H 128 " pdb=" C GLU H 128 " ideal model delta sigma weight residual 1.523 1.831 -0.308 1.34e-02 5.57e+03 5.27e+02 bond pdb=" CA GLU I 128 " pdb=" C GLU I 128 " ideal model delta sigma weight residual 1.523 1.830 -0.307 1.34e-02 5.57e+03 5.24e+02 bond pdb=" CA SER G 127 " pdb=" C SER G 127 " ideal model delta sigma weight residual 1.522 1.792 -0.270 1.20e-02 6.94e+03 5.07e+02 bond pdb=" CA SER I 127 " pdb=" C SER I 127 " ideal model delta sigma weight residual 1.522 1.792 -0.270 1.20e-02 6.94e+03 5.05e+02 ... (remaining 21871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.70: 29402 7.70 - 15.39: 239 15.39 - 23.09: 68 23.09 - 30.79: 6 30.79 - 38.49: 3 Bond angle restraints: 29718 Sorted by residual: angle pdb=" N GLU B 648 " pdb=" CA GLU B 648 " pdb=" C GLU B 648 " ideal model delta sigma weight residual 110.80 149.29 -38.49 2.13e+00 2.20e-01 3.26e+02 angle pdb=" N GLU E 648 " pdb=" CA GLU E 648 " pdb=" C GLU E 648 " ideal model delta sigma weight residual 110.80 149.20 -38.40 2.13e+00 2.20e-01 3.25e+02 angle pdb=" N GLU F 648 " pdb=" CA GLU F 648 " pdb=" C GLU F 648 " ideal model delta sigma weight residual 110.80 149.19 -38.39 2.13e+00 2.20e-01 3.25e+02 angle pdb=" O LEU D 86 " pdb=" C LEU D 86 " pdb=" N GLU D 87 " ideal model delta sigma weight residual 122.87 102.47 20.40 1.23e+00 6.61e-01 2.75e+02 angle pdb=" O LEU A 86 " pdb=" C LEU A 86 " pdb=" N GLU A 87 " ideal model delta sigma weight residual 122.87 102.50 20.37 1.23e+00 6.61e-01 2.74e+02 ... (remaining 29713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 11067 16.93 - 33.86: 399 33.86 - 50.78: 87 50.78 - 67.71: 57 67.71 - 84.64: 12 Dihedral angle restraints: 11622 sinusoidal: 4665 harmonic: 6957 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.28 76.28 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.26 76.26 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.26 76.26 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 11619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 3680 0.228 - 0.455: 175 0.455 - 0.682: 12 0.682 - 0.910: 8 0.910 - 1.137: 7 Chirality restraints: 3882 Sorted by residual: chirality pdb=" C1 MAN P 7 " pdb=" O3 MAN P 6 " pdb=" C2 MAN P 7 " pdb=" O5 MAN P 7 " both_signs ideal model delta sigma weight residual False 2.40 1.61 0.79 2.00e-02 2.50e+03 1.54e+03 chirality pdb=" C1 MAN w 7 " pdb=" O3 MAN w 6 " pdb=" C2 MAN w 7 " pdb=" O5 MAN w 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN g 7 " pdb=" O3 MAN g 6 " pdb=" C2 MAN g 7 " pdb=" O5 MAN g 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 ... (remaining 3879 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.069 2.00e-02 2.50e+03 3.47e-01 1.50e+03 pdb=" CG ASN C 301 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.236 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " -0.541 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.485 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.062 2.00e-02 2.50e+03 3.44e-01 1.48e+03 pdb=" CG ASN A 301 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.226 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " -0.537 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.486 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG z 1 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.92e+02 pdb=" C7 NAG z 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG z 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG z 1 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG z 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.10: 29 2.10 - 2.80: 5971 2.80 - 3.50: 27905 3.50 - 4.20: 51330 4.20 - 4.90: 82497 Nonbonded interactions: 167732 Sorted by model distance: nonbonded pdb=" NH1 ARG A 327 " pdb=" O ASN G 103 " model vdw 1.395 3.120 nonbonded pdb=" NH1 ARG D 327 " pdb=" O ASN H 103 " model vdw 1.416 3.120 nonbonded pdb=" CD1 ILE A 323 " pdb=" OG1 THR G 28 " model vdw 1.450 3.460 nonbonded pdb=" CD1 ILE D 323 " pdb=" OG1 THR H 28 " model vdw 1.454 3.460 nonbonded pdb=" CD1 ILE C 323 " pdb=" OG1 THR I 28 " model vdw 1.468 3.460 ... (remaining 167727 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 'T' selection = chain 'k' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '2' selection = chain '3' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'R' selection = chain 'i' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain '0' selection = chain 'T' selection = chain 'k' } pdb_interpretation.ncs_group { reference = chain '1' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain '2' selection = chain '3' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'x' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } pdb_interpretation.ncs_group { reference = chain 'R' 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.080 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1942 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 : 0.019 0.414 22110 Z= 1.270 Angle : 2.533 38.486 30372 Z= 1.396 Chirality : 0.122 1.137 3882 Planarity : 0.019 0.235 3498 Dihedral : 10.621 84.640 7029 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 2.03 % Allowed : 8.57 % Favored : 89.41 % Rotamer: Outliers : 0.57 % Allowed : 2.14 % Favored : 97.29 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2370 helix: -2.39 (0.20), residues: 417 sheet: -0.71 (0.18), residues: 774 loop : -1.76 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 98 TYR 0.015 0.001 TYR G 158 PHE 0.014 0.001 PHE G 160 TRP 0.030 0.002 TRP I 117 HIS 0.001 0.000 HIS I 234 Details of bonding type rmsd/Z covalent geometry : bond 0.01621 / 1.12 (21876) covalent geometry : angle 2.22887 / 1.34 (29718) SS BOND : bond 0.13397 / 8.48 ( 39) SS BOND : angle 7.88538 / 5.99 ( 78) hydrogen bonds : bond 0.20788 / 13.95 ( 696) hydrogen bonds : angle 8.64014 / 5.99 ( 1872) Misc. bond : bond 0.29409 / 14.76 ( 3) link_ALPHA1-2 : bond 0.01891 / 1.06 ( 12) link_ALPHA1-2 : angle 4.74840 / 3.03 ( 36) link_ALPHA1-3 : bond 0.04394 / 2.85 ( 21) link_ALPHA1-3 : angle 7.37149 / 4.80 ( 63) link_ALPHA1-6 : bond 0.03731 / 2.27 ( 18) link_ALPHA1-6 : angle 5.27714 / 3.72 ( 54) link_BETA1-4 : bond 0.04127 / 2.62 ( 81) link_BETA1-4 : angle 5.87075 / 4.05 ( 243) link_NAG-ASN : bond 0.14980 / 10.00 ( 60) link_NAG-ASN : angle 12.52510 / 8.87 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 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: 0.0010 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 : 0.001 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 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: -0.0672 (tpt) cc_final: -0.1985 (tpt) REVERT: A 197 ASN cc_start: 0.3076 (OUTLIER) cc_final: 0.2838 (p0) REVERT: A 279 ASN cc_start: 0.6977 (t0) cc_final: 0.4950 (m-40) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.0905 time to fit residues: 5.9595 Evaluate side-chains 25 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.125 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.7571 (m-30) cc_final: 0.6344 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0650 time to fit residues: 2.4237 Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.041 Evaluate side-chains 42 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 6 GLN cc_start: 0.6342 (mt0) cc_final: 0.5140 (mp10) REVERT: G 73 ASP cc_start: 0.4495 (t0) cc_final: 0.4133 (m-30) REVERT: G 160 PHE cc_start: 0.7848 (t80) cc_final: 0.7189 (t80) REVERT: G 210 PHE cc_start: 0.4230 (m-80) cc_final: 0.3608 (m-80) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1023 time to fit residues: 4.6197 Evaluate side-chains 25 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.069 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 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: 237 random chunks: chunk 216 optimal weight: 0.0370 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.1980 chunk 235 optimal weight: 0.0000 overall best weight: 0.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** G 219 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109906 restraints weight = 1427.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111456 restraints weight = 896.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.111992 restraints weight = 665.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112513 restraints weight = 561.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112767 restraints weight = 491.419| |-----------------------------------------------------------------------------| r_work (final): 0.3634 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101157 restraints weight = 224.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101872 restraints weight = 97.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102231 restraints weight = 52.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102417 restraints weight = 29.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102538 restraints weight = 17.616| |-----------------------------------------------------------------------------| r_work (final): 0.3245 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.078563 restraints weight = 407.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.076661 restraints weight = 622.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.075846 restraints weight = 841.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.075493 restraints weight = 1000.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.075493 restraints weight = 1089.344| |-----------------------------------------------------------------------------| r_work (final): 0.2785 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.124791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.108740 restraints weight = 19037.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.110824 restraints weight = 14386.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.112250 restraints weight = 11386.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.113624 restraints weight = 9528.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.114584 restraints weight = 8088.962| |-----------------------------------------------------------------------------| r_work (final): 0.4425 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.132148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.119355 restraints weight = 6855.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.119679 restraints weight = 6395.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.119679 restraints weight = 6114.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.119679 restraints weight = 6114.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.119679 restraints weight = 6114.722| |-----------------------------------------------------------------------------| r_work (final): 0.4175 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.134278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.123269 restraints weight = 12587.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.124893 restraints weight = 9973.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.126181 restraints weight = 8097.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.127174 restraints weight = 6754.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.127841 restraints weight = 5712.837| |-----------------------------------------------------------------------------| r_work (final): 0.4562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141493 restraints weight = 579.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.142437 restraints weight = 477.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143015 restraints weight = 409.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143015 restraints weight = 366.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143015 restraints weight = 366.572| |-----------------------------------------------------------------------------| r_work (final): 0.4034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101940 restraints weight = 522.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102475 restraints weight = 252.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102728 restraints weight = 137.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102952 restraints weight = 76.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103084 restraints weight = 42.369| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3038 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 1.045 22110 Z= 1.399 Angle : 3.070 52.480 30372 Z= 1.184 Chirality : 0.263 4.234 3882 Planarity : 0.010 0.100 3498 Dihedral : 6.411 35.158 2598 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 35.14 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.99 % Favored : 90.25 % Rotamer: Outliers : 0.86 % Allowed : 3.43 % Favored : 95.71 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.05 (0.16), residues: 2370 helix: -1.55 (0.23), residues: 408 sheet: -0.73 (0.17), residues: 849 loop : -1.73 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 145 TYR 0.039 0.005 TYR D 40 PHE 0.103 0.006 PHE H 194 TRP 0.071 0.004 TRP B 571 HIS 0.012 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.01685 / 0.84 (21876) covalent geometry : angle 2.59268 / 1.05 (29718) SS BOND : bond 0.01921 / 1.24 ( 39) SS BOND : angle 5.54798 / 4.84 ( 78) hydrogen bonds : bond 0.08549 / 5.98 ( 696) hydrogen bonds : angle 7.35218 / 5.14 ( 1872) Misc. bond : bond 0.02146 / 1.07 ( 3) link_ALPHA1-2 : bond 0.29173 / 20.56 ( 12) link_ALPHA1-2 : angle 11.51106 / 9.12 ( 36) link_ALPHA1-3 : bond 0.44785 / 26.58 ( 21) link_ALPHA1-3 : angle 20.78435 / 13.54 ( 63) link_ALPHA1-6 : bond 0.56495 / 32.94 ( 18) link_ALPHA1-6 : angle 23.18216 / 18.10 ( 54) link_BETA1-4 : bond 0.02356 / 1.46 ( 81) link_BETA1-4 : angle 3.83724 / 2.62 ( 243) link_NAG-ASN : bond 0.03714 / 2.32 ( 60) link_NAG-ASN : angle 10.39726 / 6.94 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0033 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: 0.0017 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 Evaluate side-chains 39 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6018 (ppp) cc_final: 0.5576 (ppp) REVERT: A 161 MET cc_start: -0.3267 (tpt) cc_final: -0.3919 (tpt) REVERT: A 383 PHE cc_start: 0.6751 (m-10) cc_final: 0.6252 (m-10) REVERT: A 434 MET cc_start: -0.0943 (tmm) cc_final: -0.1419 (ttt) REVERT: A 442 VAL cc_start: 0.4603 (OUTLIER) cc_final: 0.4390 (m) REVERT: A 483 LEU cc_start: 0.8578 (mt) cc_final: 0.8274 (mt) REVERT: A 486 TYR cc_start: 0.7401 (m-10) cc_final: 0.6407 (m-80) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.0847 time to fit residues: 3.9815 Evaluate side-chains 27 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.160 Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: E 586 TYR cc_start: 0.6115 (t80) cc_final: 0.5843 (t80) REVERT: E 650 GLN cc_start: 0.8033 (tt0) cc_final: 0.7383 (pm20) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0651 time to fit residues: 1.7939 Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.043 Evaluate side-chains 34 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 6 GLN cc_start: 0.7555 (mt0) cc_final: 0.6019 (mp10) REVERT: G 78 THR cc_start: 0.4859 (p) cc_final: 0.4290 (p) REVERT: G 131 MET cc_start: 0.3209 (mtm) cc_final: 0.2716 (ptp) REVERT: G 158 TYR cc_start: 0.5423 (t80) cc_final: 0.3256 (m-80) REVERT: G 210 PHE cc_start: 0.4876 (m-80) cc_final: 0.3957 (m-10) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.0660 time to fit residues: 2.6129 Evaluate side-chains 27 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.069 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 150 optimal weight: 6.9990 chunk 145 optimal weight: 0.0000 chunk 9 optimal weight: 0.0970 chunk 200 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 0.0020 chunk 222 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 35 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.125023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.119293 restraints weight = 570.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119722 restraints weight = 480.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119719 restraints weight = 429.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119719 restraints weight = 428.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119719 restraints weight = 428.815| |-----------------------------------------------------------------------------| r_work (final): 0.3736 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094907 restraints weight = 465.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095706 restraints weight = 219.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096141 restraints weight = 113.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096372 restraints weight = 58.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096491 restraints weight = 32.145| |-----------------------------------------------------------------------------| r_work (final): 0.3281 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092402 restraints weight = 318.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092402 restraints weight = 289.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092402 restraints weight = 289.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092402 restraints weight = 289.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092402 restraints weight = 289.614| |-----------------------------------------------------------------------------| r_work (final): 0.2940 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.127311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.112314 restraints weight = 20650.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.114383 restraints weight = 15933.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.115860 restraints weight = 12691.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.117008 restraints weight = 10524.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.117711 restraints weight = 9017.619| |-----------------------------------------------------------------------------| r_work (final): 0.4472 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.128266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.113416 restraints weight = 5482.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.113900 restraints weight = 4745.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.114272 restraints weight = 4350.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.114272 restraints weight = 4091.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.114272 restraints weight = 4090.937| |-----------------------------------------------------------------------------| r_work (final): 0.4128 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.120947 restraints weight = 13123.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.122505 restraints weight = 10096.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.123768 restraints weight = 8047.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.124473 restraints weight = 6559.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.125467 restraints weight = 5614.746| |-----------------------------------------------------------------------------| r_work (final): 0.4505 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146075 restraints weight = 442.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.146239 restraints weight = 177.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.146343 restraints weight = 98.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.146379 restraints weight = 41.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146420 restraints weight = 25.811| |-----------------------------------------------------------------------------| r_work (final): 0.4215 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106338 restraints weight = 541.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106717 restraints weight = 183.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106875 restraints weight = 68.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.106956 restraints weight = 31.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.106959 restraints weight = 14.828| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2885 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 1.029 22110 Z= 1.251 Angle : 2.479 40.853 30372 Z= 0.959 Chirality : 0.155 4.260 3882 Planarity : 0.018 0.496 3498 Dihedral : 7.298 79.231 2598 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 32.63 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.11 % Favored : 90.38 % Rotamer: Outliers : 0.29 % Allowed : 3.57 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.18 (0.16), residues: 2370 helix: -1.45 (0.23), residues: 411 sheet: -0.85 (0.17), residues: 861 loop : -1.87 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG H 145 TYR 0.024 0.003 TYR B 638 PHE 0.056 0.003 PHE H 194 TRP 0.035 0.004 TRP F 571 HIS 0.003 0.001 HIS I 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01283 / 0.64 (21876) covalent geometry : angle 1.93392 / 0.81 (29718) SS BOND : bond 0.01373 / 0.92 ( 39) SS BOND : angle 3.25669 / 2.73 ( 78) hydrogen bonds : bond 0.07909 / 5.45 ( 696) hydrogen bonds : angle 7.14737 / 4.99 ( 1872) Misc. bond : bond 0.01980 / 1.00 ( 3) link_ALPHA1-2 : bond 0.25604 / 18.04 ( 12) link_ALPHA1-2 : angle 13.03038 / 10.46 ( 36) link_ALPHA1-3 : bond 0.41623 / 24.48 ( 21) link_ALPHA1-3 : angle 19.28152 / 12.53 ( 63) link_ALPHA1-6 : bond 0.56652 / 33.07 ( 18) link_ALPHA1-6 : angle 20.64415 / 16.24 ( 54) link_BETA1-4 : bond 0.01681 / 1.06 ( 81) link_BETA1-4 : angle 3.65806 / 2.57 ( 243) link_NAG-ASN : bond 0.03211 / 2.26 ( 60) link_NAG-ASN : angle 10.25732 / 6.79 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 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: 0.0009 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 : 0.001 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 37 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 300 ASN cc_start: 0.4459 (m110) cc_final: 0.3423 (m-40) REVERT: D 434 MET cc_start: -0.5831 (tmm) cc_final: -0.6492 (ttt) REVERT: D 486 TYR cc_start: 0.6397 (m-10) cc_final: 0.5633 (m-80) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0870 time to fit residues: 3.9489 Evaluate side-chains 23 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.134 Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.040 Fit side-chains REVERT: E 589 ASP cc_start: 0.8109 (m-30) cc_final: 0.7876 (m-30) REVERT: E 632 ASP cc_start: 0.3921 (t0) cc_final: 0.2874 (p0) REVERT: E 650 GLN cc_start: 0.7832 (tt0) cc_final: 0.7340 (pm20) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.0700 time to fit residues: 1.8506 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.040 Evaluate side-chains 30 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 6 GLN cc_start: 0.7322 (mt0) cc_final: 0.5999 (mp10) REVERT: G 27 TYR cc_start: 0.5314 (p90) cc_final: 0.4511 (t80) REVERT: G 48 MET cc_start: 0.6213 (mpp) cc_final: 0.5800 (mpp) REVERT: G 78 THR cc_start: 0.4391 (p) cc_final: 0.4188 (p) REVERT: G 158 TYR cc_start: 0.5232 (t80) cc_final: 0.3348 (m-80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0774 time to fit residues: 2.6502 Evaluate side-chains 24 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.068 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 202 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 35 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.122825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.114711 restraints weight = 1329.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.116088 restraints weight = 871.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117013 restraints weight = 668.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.117471 restraints weight = 550.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.117594 restraints weight = 482.161| |-----------------------------------------------------------------------------| r_work (final): 0.4025 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.090020 restraints weight = 403.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090668 restraints weight = 128.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090996 restraints weight = 58.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091128 restraints weight = 29.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091247 restraints weight = 15.127| |-----------------------------------------------------------------------------| r_work (final): 0.3167 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094549 restraints weight = 361.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094593 restraints weight = 340.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094593 restraints weight = 335.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094593 restraints weight = 335.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094593 restraints weight = 335.690| |-----------------------------------------------------------------------------| r_work (final): 0.3004 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.125975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.110595 restraints weight = 20335.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.112437 restraints weight = 15516.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.114060 restraints weight = 12488.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.115159 restraints weight = 10329.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.116028 restraints weight = 8900.835| |-----------------------------------------------------------------------------| r_work (final): 0.4448 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.129504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.114708 restraints weight = 5835.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.115161 restraints weight = 5260.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.115164 restraints weight = 4904.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.115573 restraints weight = 4901.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.115682 restraints weight = 4692.489| |-----------------------------------------------------------------------------| r_work (final): 0.4124 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.122168 restraints weight = 12835.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.123771 restraints weight = 9996.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.125051 restraints weight = 7987.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.125816 restraints weight = 6502.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.126893 restraints weight = 5519.723| |-----------------------------------------------------------------------------| r_work (final): 0.4530 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122120 restraints weight = 706.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122117 restraints weight = 715.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122117 restraints weight = 715.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122117 restraints weight = 715.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122117 restraints weight = 715.365| |-----------------------------------------------------------------------------| r_work (final): 0.3841 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105104 restraints weight = 559.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105456 restraints weight = 370.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105679 restraints weight = 250.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105838 restraints weight = 180.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105966 restraints weight = 111.157| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2970 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 1.002 22110 Z= 1.223 Angle : 2.364 41.240 30372 Z= 0.907 Chirality : 0.157 4.084 3882 Planarity : 0.014 0.335 3498 Dihedral : 7.122 37.681 2598 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.61 % Favored : 90.89 % Rotamer: Outliers : 0.43 % Allowed : 2.57 % Favored : 97.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.22 (0.16), residues: 2370 helix: -1.20 (0.24), residues: 384 sheet: -0.91 (0.17), residues: 852 loop : -1.99 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG D 503 TYR 0.026 0.003 TYR B 643 PHE 0.062 0.004 PHE H 101 TRP 0.026 0.004 TRP B 571 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01206 / 0.59 (21876) covalent geometry : angle 1.75461 / 0.74 (29718) SS BOND : bond 0.01957 / 1.44 ( 39) SS BOND : angle 4.31770 / 3.15 ( 78) hydrogen bonds : bond 0.07071 / 4.88 ( 696) hydrogen bonds : angle 7.07014 / 4.91 ( 1872) Misc. bond : bond 0.03776 / 1.88 ( 3) link_ALPHA1-2 : bond 0.24086 / 16.97 ( 12) link_ALPHA1-2 : angle 12.69320 / 10.25 ( 36) link_ALPHA1-3 : bond 0.42256 / 24.70 ( 21) link_ALPHA1-3 : angle 19.87115 / 13.02 ( 63) link_ALPHA1-6 : bond 0.55758 / 32.56 ( 18) link_ALPHA1-6 : angle 20.80969 / 16.38 ( 54) link_BETA1-4 : bond 0.01438 / 0.90 ( 81) link_BETA1-4 : angle 3.93143 / 2.73 ( 243) link_NAG-ASN : bond 0.02986 / 2.06 ( 60) link_NAG-ASN : angle 10.25918 / 6.74 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 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: 0.0009 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 : 0.001 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 33 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 330 HIS cc_start: 0.7626 (p90) cc_final: 0.7092 (p90) REVERT: D 434 MET cc_start: -0.5726 (tmm) cc_final: -0.6481 (ttt) REVERT: D 486 TYR cc_start: 0.6363 (m-10) cc_final: 0.5550 (m-80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0687 time to fit residues: 2.8510 Evaluate side-chains 24 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.094 Evaluate side-chains 22 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.040 Fit side-chains REVERT: E 590 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6337 (tm-30) REVERT: E 632 ASP cc_start: 0.5228 (t0) cc_final: 0.3491 (p0) REVERT: E 650 GLN cc_start: 0.7941 (tt0) cc_final: 0.7513 (pm20) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0653 time to fit residues: 1.5943 Evaluate side-chains 17 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.040 Evaluate side-chains 30 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: G 6 GLN cc_start: 0.7960 (mt0) cc_final: 0.7010 (mp10) REVERT: G 48 MET cc_start: 0.6364 (mpp) cc_final: 0.5843 (mpp) REVERT: G 131 MET cc_start: 0.2853 (mtm) cc_final: 0.2263 (ttp) REVERT: G 158 TYR cc_start: 0.4648 (t80) cc_final: 0.2285 (m-80) REVERT: G 216 GLN cc_start: 0.4275 (tp-100) cc_final: 0.3941 (tp-100) outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.0771 time to fit residues: 2.6553 Evaluate side-chains 21 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.066 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: 0.0019 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 0.0770 chunk 156 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 179 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.116582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110909 restraints weight = 1024.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112104 restraints weight = 616.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112766 restraints weight = 448.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113183 restraints weight = 362.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113404 restraints weight = 312.654| |-----------------------------------------------------------------------------| r_work (final): 0.3701 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119721 restraints weight = 132.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120509 restraints weight = 39.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.120901 restraints weight = 17.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121163 restraints weight = 9.567 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121283 restraints weight = 5.325 | |-----------------------------------------------------------------------------| r_work (final): 0.3777 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088826 restraints weight = 256.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090140 restraints weight = 197.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090938 restraints weight = 169.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091451 restraints weight = 151.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091791 restraints weight = 139.933| |-----------------------------------------------------------------------------| r_work (final): 0.3277 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.126061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.111035 restraints weight = 20535.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.113068 restraints weight = 15658.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.114127 restraints weight = 12427.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.115481 restraints weight = 10621.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.116387 restraints weight = 9089.732| |-----------------------------------------------------------------------------| r_work (final): 0.4456 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.113216 restraints weight = 5503.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113985 restraints weight = 4628.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.114522 restraints weight = 4093.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.114808 restraints weight = 3817.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.114808 restraints weight = 3641.742| |-----------------------------------------------------------------------------| r_work (final): 0.4159 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.134915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.123661 restraints weight = 12638.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.125162 restraints weight = 10152.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.126301 restraints weight = 8422.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.127287 restraints weight = 7199.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.128068 restraints weight = 6195.226| |-----------------------------------------------------------------------------| r_work (final): 0.4541 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123565 restraints weight = 7698.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123565 restraints weight = 8775.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123565 restraints weight = 8774.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123565 restraints weight = 8774.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123565 restraints weight = 8774.904| |-----------------------------------------------------------------------------| r_work (final): 0.3633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.120680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118175 restraints weight = 485.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.118953 restraints weight = 299.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119457 restraints weight = 201.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.119716 restraints weight = 139.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119947 restraints weight = 102.622| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3082 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.985 22110 Z= 1.198 Angle : 2.275 41.916 30372 Z= 0.860 Chirality : 0.153 3.815 3882 Planarity : 0.010 0.154 3498 Dihedral : 6.943 35.100 2598 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.73 % Favored : 90.76 % Rotamer: Outliers : 0.29 % Allowed : 1.43 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.09 (0.16), residues: 2370 helix: -0.93 (0.25), residues: 384 sheet: -0.71 (0.17), residues: 849 loop : -2.07 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 327 TYR 0.037 0.003 TYR D 217 PHE 0.068 0.004 PHE I 101 TRP 0.019 0.003 TRP E 571 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01111 / 0.55 (21876) covalent geometry : angle 1.65583 / 0.69 (29718) SS BOND : bond 0.01595 / 1.17 ( 39) SS BOND : angle 3.16143 / 2.35 ( 78) hydrogen bonds : bond 0.06147 / 4.26 ( 696) hydrogen bonds : angle 6.89795 / 4.78 ( 1872) Misc. bond : bond 0.02042 / 1.02 ( 3) link_ALPHA1-2 : bond 0.23682 / 16.69 ( 12) link_ALPHA1-2 : angle 13.05449 / 10.57 ( 36) link_ALPHA1-3 : bond 0.42529 / 24.73 ( 21) link_ALPHA1-3 : angle 20.09462 / 13.16 ( 63) link_ALPHA1-6 : bond 0.55272 / 32.29 ( 18) link_ALPHA1-6 : angle 20.94461 / 16.48 ( 54) link_BETA1-4 : bond 0.01261 / 0.79 ( 81) link_BETA1-4 : angle 3.71745 / 2.62 ( 243) link_NAG-ASN : bond 0.02676 / 1.82 ( 60) link_NAG-ASN : angle 9.51847 / 6.14 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 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 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 : 0.001 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 30 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5674 (tmm) cc_final: -0.6467 (ttt) REVERT: D 486 TYR cc_start: 0.6265 (m-10) cc_final: 0.5688 (m-80) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0856 time to fit residues: 3.1932 Evaluate side-chains 22 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.170 Evaluate side-chains 22 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.042 Fit side-chains REVERT: E 650 GLN cc_start: 0.8125 (tt0) cc_final: 0.7739 (pm20) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0754 time to fit residues: 1.8250 Evaluate side-chains 16 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.044 Evaluate side-chains 32 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: G 131 MET cc_start: 0.2708 (mtm) cc_final: 0.2319 (ttp) REVERT: G 158 TYR cc_start: 0.4565 (t80) cc_final: 0.2371 (m-80) REVERT: G 226 THR cc_start: 0.6183 (t) cc_final: 0.4947 (t) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0704 time to fit residues: 2.5991 Evaluate side-chains 20 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.065 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 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: 0.0026 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: 237 random chunks: chunk 153 optimal weight: 10.0000 chunk 205 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 152 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 228 optimal weight: 0.0040 chunk 230 optimal weight: 0.4980 chunk 93 optimal weight: 0.3980 chunk 76 optimal weight: 0.0270 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 159 ASN ** G 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.123182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121635 restraints weight = 823.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121670 restraints weight = 739.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121670 restraints weight = 715.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.121733 restraints weight = 715.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.121883 restraints weight = 668.949| |-----------------------------------------------------------------------------| r_work (final): 0.3770 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082597 restraints weight = 398.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082864 restraints weight = 78.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082964 restraints weight = 20.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082966 restraints weight = 5.149 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082970 restraints weight = 1.294 | |-----------------------------------------------------------------------------| r_work (final): 0.3226 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090346 restraints weight = 274.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092401 restraints weight = 188.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093509 restraints weight = 151.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094595 restraints weight = 126.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095138 restraints weight = 103.398| |-----------------------------------------------------------------------------| r_work (final): 0.3348 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.126485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.111455 restraints weight = 20442.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.113476 restraints weight = 15491.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.114851 restraints weight = 12259.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.116059 restraints weight = 10204.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.116465 restraints weight = 8706.209| |-----------------------------------------------------------------------------| r_work (final): 0.4458 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.131529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.111623 restraints weight = 7047.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.113872 restraints weight = 4916.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.115167 restraints weight = 3913.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.115813 restraints weight = 3362.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.115817 restraints weight = 3090.611| |-----------------------------------------------------------------------------| r_work (final): 0.4125 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.132743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.121784 restraints weight = 12275.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.123723 restraints weight = 9314.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.125236 restraints weight = 7319.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.126447 restraints weight = 5849.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.127360 restraints weight = 4770.179| |-----------------------------------------------------------------------------| r_work (final): 0.4518 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.139877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131169 restraints weight = 4608.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135882 restraints weight = 3095.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.136979 restraints weight = 2411.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136475 restraints weight = 2594.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.136532 restraints weight = 2658.896| |-----------------------------------------------------------------------------| r_work (final): 0.3946 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.115083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110274 restraints weight = 541.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110304 restraints weight = 438.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110346 restraints weight = 434.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110346 restraints weight = 429.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110346 restraints weight = 429.126| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2977 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 : 0.024 0.973 22110 Z= 1.191 Angle : 2.245 41.879 30372 Z= 0.845 Chirality : 0.150 3.606 3882 Planarity : 0.013 0.374 3498 Dihedral : 7.067 43.551 2598 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.11 % Favored : 90.51 % Rotamer: Outliers : 0.14 % Allowed : 2.57 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.09 (0.16), residues: 2370 helix: -0.90 (0.26), residues: 366 sheet: -0.64 (0.17), residues: 852 loop : -2.14 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 327 TYR 0.028 0.003 TYR G 163 PHE 0.032 0.003 PHE H 101 TRP 0.033 0.003 TRP D 479 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.55 (21876) covalent geometry : angle 1.61100 / 0.67 (29718) SS BOND : bond 0.01021 / 0.75 ( 39) SS BOND : angle 2.62524 / 1.99 ( 78) hydrogen bonds : bond 0.05967 / 4.16 ( 696) hydrogen bonds : angle 6.77603 / 4.69 ( 1872) Misc. bond : bond 0.03551 / 1.71 ( 3) link_ALPHA1-2 : bond 0.23439 / 16.52 ( 12) link_ALPHA1-2 : angle 13.26625 / 10.76 ( 36) link_ALPHA1-3 : bond 0.42710 / 24.76 ( 21) link_ALPHA1-3 : angle 20.29959 / 13.28 ( 63) link_ALPHA1-6 : bond 0.54784 / 32.01 ( 18) link_ALPHA1-6 : angle 21.10372 / 16.62 ( 54) link_BETA1-4 : bond 0.01236 / 0.78 ( 81) link_BETA1-4 : angle 3.59747 / 2.55 ( 243) link_NAG-ASN : bond 0.01879 / 1.29 ( 60) link_NAG-ASN : angle 9.39573 / 6.11 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 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: 0.0010 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 : 0.001 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 28 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5668 (tmm) cc_final: -0.6454 (ttt) REVERT: D 486 TYR cc_start: 0.6367 (m-80) cc_final: 0.5730 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0695 time to fit residues: 2.5110 Evaluate side-chains 19 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.128 Evaluate side-chains 22 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.041 Fit side-chains REVERT: E 530 MET cc_start: 0.4099 (ptp) cc_final: 0.1285 (ptm) REVERT: E 650 GLN cc_start: 0.8365 (tt0) cc_final: 0.7783 (pm20) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0717 time to fit residues: 1.7338 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.040 Evaluate side-chains 26 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: G 158 TYR cc_start: 0.4704 (t80) cc_final: 0.2249 (m-80) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0614 time to fit residues: 1.9004 Evaluate side-chains 17 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 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: 0.0013 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: 0.0016 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 207 optimal weight: 0.0770 chunk 16 optimal weight: 0.0970 chunk 210 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 422 GLN G 35 HIS ** G 219 ASN ** 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 = 0.3897 r_free = 0.3897 target = 0.122610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121252 restraints weight = 759.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121251 restraints weight = 714.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121251 restraints weight = 714.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121251 restraints weight = 714.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121251 restraints weight = 714.027| |-----------------------------------------------------------------------------| r_work (final): 0.3771 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.084123 restraints weight = 305.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084638 restraints weight = 103.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084812 restraints weight = 32.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084880 restraints weight = 9.800 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084882 restraints weight = 2.963 | |-----------------------------------------------------------------------------| r_work (final): 0.3284 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082650 restraints weight = 264.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085673 restraints weight = 179.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086969 restraints weight = 136.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088064 restraints weight = 111.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088731 restraints weight = 90.807| |-----------------------------------------------------------------------------| r_work (final): 0.3277 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.124770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.109551 restraints weight = 20229.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.111477 restraints weight = 15332.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.112908 restraints weight = 12183.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.113980 restraints weight = 10101.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.114787 restraints weight = 8723.934| |-----------------------------------------------------------------------------| r_work (final): 0.4423 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.128078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.112324 restraints weight = 5540.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.113267 restraints weight = 4623.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.113985 restraints weight = 4070.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.114365 restraints weight = 3727.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.114365 restraints weight = 3520.833| |-----------------------------------------------------------------------------| r_work (final): 0.4164 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.131503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.120740 restraints weight = 12115.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.122515 restraints weight = 9274.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.123964 restraints weight = 7333.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.125230 restraints weight = 5917.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.126197 restraints weight = 4779.880| |-----------------------------------------------------------------------------| r_work (final): 0.4512 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121463 restraints weight = 307.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122296 restraints weight = 254.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122659 restraints weight = 230.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122658 restraints weight = 218.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122658 restraints weight = 218.693| |-----------------------------------------------------------------------------| r_work (final): 0.3936 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.116426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112384 restraints weight = 548.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112396 restraints weight = 547.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112396 restraints weight = 543.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112396 restraints weight = 543.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112396 restraints weight = 543.114| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3114 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.968 22110 Z= 1.183 Angle : 2.206 41.985 30372 Z= 0.821 Chirality : 0.156 3.899 3882 Planarity : 0.011 0.241 3498 Dihedral : 6.849 31.340 2598 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.73 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.12 (0.16), residues: 2370 helix: -0.79 (0.26), residues: 366 sheet: -0.52 (0.18), residues: 810 loop : -2.29 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 327 TYR 0.021 0.002 TYR C 39 PHE 0.066 0.003 PHE G 227 TRP 0.016 0.002 TRP G 47 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01070 / 0.53 (21876) covalent geometry : angle 1.56198 / 0.64 (29718) SS BOND : bond 0.01340 / 0.92 ( 39) SS BOND : angle 2.42058 / 1.85 ( 78) hydrogen bonds : bond 0.05480 / 3.79 ( 696) hydrogen bonds : angle 6.84368 / 4.72 ( 1872) Misc. bond : bond 0.01867 / 0.94 ( 3) link_ALPHA1-2 : bond 0.23288 / 16.41 ( 12) link_ALPHA1-2 : angle 13.41761 / 10.89 ( 36) link_ALPHA1-3 : bond 0.42806 / 24.77 ( 21) link_ALPHA1-3 : angle 20.45802 / 13.36 ( 63) link_ALPHA1-6 : bond 0.54621 / 31.92 ( 18) link_ALPHA1-6 : angle 21.18211 / 16.69 ( 54) link_BETA1-4 : bond 0.01232 / 0.78 ( 81) link_BETA1-4 : angle 3.38069 / 2.39 ( 243) link_NAG-ASN : bond 0.02260 / 1.64 ( 60) link_NAG-ASN : angle 9.12455 / 5.85 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 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: 0.0009 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 : 0.001 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 27 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5453 (tmm) cc_final: -0.6275 (ttt) REVERT: D 475 MET cc_start: 0.6589 (mmp) cc_final: 0.5199 (tmm) REVERT: D 486 TYR cc_start: 0.6383 (m-80) cc_final: 0.5733 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0653 time to fit residues: 2.2562 Evaluate side-chains 20 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.126 Evaluate side-chains 20 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.041 Fit side-chains REVERT: E 530 MET cc_start: 0.3655 (ptp) cc_final: 0.0895 (ptm) REVERT: E 650 GLN cc_start: 0.8014 (tt0) cc_final: 0.7661 (pm20) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0622 time to fit residues: 1.4030 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.047 Evaluate side-chains 22 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: G 158 TYR cc_start: 0.4829 (t80) cc_final: 0.2331 (m-10) REVERT: G 218 TYR cc_start: 0.5817 (p90) cc_final: 0.5564 (p90) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0473 time to fit residues: 1.2911 Evaluate side-chains 16 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.066 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 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 46 optimal weight: 0.0070 chunk 1 optimal weight: 0.0060 chunk 160 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 127 optimal weight: 0.0570 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 234 ASN G 165 GLN ** G 219 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.117895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.112313 restraints weight = 1421.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.113338 restraints weight = 974.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.114062 restraints weight = 740.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114425 restraints weight = 597.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114425 restraints weight = 520.477| |-----------------------------------------------------------------------------| r_work (final): 0.3685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.081212 restraints weight = 265.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.081708 restraints weight = 79.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081852 restraints weight = 25.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081906 restraints weight = 7.541 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081923 restraints weight = 2.494 | |-----------------------------------------------------------------------------| r_work (final): 0.3259 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078704 restraints weight = 298.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081850 restraints weight = 197.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083517 restraints weight = 149.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084391 restraints weight = 108.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084935 restraints weight = 86.131| |-----------------------------------------------------------------------------| r_work (final): 0.3125 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.125301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.109801 restraints weight = 20546.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.111796 restraints weight = 15493.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.113306 restraints weight = 12255.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.114378 restraints weight = 10124.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.115253 restraints weight = 8732.615| |-----------------------------------------------------------------------------| r_work (final): 0.4425 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.127707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.103931 restraints weight = 5629.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.106087 restraints weight = 4237.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.107522 restraints weight = 3318.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.108515 restraints weight = 2753.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.109172 restraints weight = 2401.297| |-----------------------------------------------------------------------------| r_work (final): 0.4041 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.130540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.119815 restraints weight = 12488.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.121872 restraints weight = 9405.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.123371 restraints weight = 7278.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.124445 restraints weight = 5858.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.125397 restraints weight = 4853.187| |-----------------------------------------------------------------------------| r_work (final): 0.4514 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151452 restraints weight = 4598.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.151915 restraints weight = 3457.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152189 restraints weight = 2710.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154082 restraints weight = 2791.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155385 restraints weight = 2338.595| |-----------------------------------------------------------------------------| r_work (final): 0.4058 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.119472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.114506 restraints weight = 620.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114677 restraints weight = 582.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114678 restraints weight = 553.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114678 restraints weight = 553.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114678 restraints weight = 553.529| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3011 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.700 22110 Z= 1.538 Angle : 2.299 70.320 30372 Z= 0.842 Chirality : 0.151 3.531 3882 Planarity : 0.010 0.190 3498 Dihedral : 6.722 30.437 2598 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.23 % Favored : 91.39 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.29 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.00 (0.16), residues: 2370 helix: -0.71 (0.26), residues: 366 sheet: -0.42 (0.18), residues: 786 loop : -2.20 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 327 TYR 0.018 0.002 TYR D 39 PHE 0.031 0.002 PHE H 227 TRP 0.040 0.002 TRP G 162 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.52 (21876) covalent geometry : angle 1.52585 / 0.62 (29718) SS BOND : bond 0.00881 / 0.61 ( 39) SS BOND : angle 2.20601 / 1.68 ( 78) hydrogen bonds : bond 0.05132 / 3.56 ( 696) hydrogen bonds : angle 6.73328 / 4.64 ( 1872) Misc. bond : bond 0.01604 / 0.82 ( 3) link_ALPHA1-2 : bond 0.23157 / 16.32 ( 12) link_ALPHA1-2 : angle 13.56486 / 11.02 ( 36) link_ALPHA1-3 : bond 0.42867 / 24.77 ( 21) link_ALPHA1-3 : angle 20.57211 / 13.42 ( 63) link_ALPHA1-6 : bond 0.54389 / 31.78 ( 18) link_ALPHA1-6 : angle 21.30212 / 16.80 ( 54) link_BETA1-4 : bond 0.01109 / 0.70 ( 81) link_BETA1-4 : angle 3.22309 / 2.30 ( 243) link_NAG-ASN : bond 0.38053 / 23.74 ( 60) link_NAG-ASN : angle 13.05388 / 8.31 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 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 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 : 0.001 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 28 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5502 (tmm) cc_final: -0.6325 (ttt) REVERT: D 475 MET cc_start: 0.6523 (mmp) cc_final: 0.5186 (tmm) REVERT: D 486 TYR cc_start: 0.6373 (m-80) cc_final: 0.5774 (m-80) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0728 time to fit residues: 2.6416 Evaluate side-chains 17 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.138 Evaluate side-chains 22 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.042 Fit side-chains REVERT: E 530 MET cc_start: 0.5134 (ptp) cc_final: 0.2828 (ptm) REVERT: E 586 TYR cc_start: 0.7592 (t80) cc_final: 0.7337 (t80) REVERT: E 587 LEU cc_start: 0.9283 (mm) cc_final: 0.8956 (pp) REVERT: E 614 TRP cc_start: 0.5875 (m-90) cc_final: 0.5567 (m100) REVERT: E 650 GLN cc_start: 0.8681 (tt0) cc_final: 0.7951 (pm20) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0658 time to fit residues: 1.6057 Evaluate side-chains 16 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.052 Evaluate side-chains 21 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: G 158 TYR cc_start: 0.4710 (t80) cc_final: 0.2350 (m-10) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0477 time to fit residues: 1.2642 Evaluate side-chains 16 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.062 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 122 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 189 optimal weight: 0.0370 chunk 191 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 0.0060 chunk 84 optimal weight: 0.0040 overall best weight: 0.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 219 ASN ** 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 = 0.3861 r_free = 0.3861 target = 0.119627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117310 restraints weight = 774.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117311 restraints weight = 746.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117328 restraints weight = 744.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117328 restraints weight = 736.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117328 restraints weight = 736.906| |-----------------------------------------------------------------------------| r_work (final): 0.3752 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.080663 restraints weight = 305.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.081378 restraints weight = 98.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081657 restraints weight = 37.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.081769 restraints weight = 14.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.081802 restraints weight = 6.632 | |-----------------------------------------------------------------------------| r_work (final): 0.3218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079374 restraints weight = 261.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082340 restraints weight = 186.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083540 restraints weight = 130.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084290 restraints weight = 98.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084826 restraints weight = 77.950| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.109804 restraints weight = 21076.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.111610 restraints weight = 16053.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.113082 restraints weight = 12914.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.114177 restraints weight = 10763.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.114992 restraints weight = 9253.588| |-----------------------------------------------------------------------------| r_work (final): 0.4431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.128957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.110700 restraints weight = 6937.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.112942 restraints weight = 4678.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.114064 restraints weight = 3663.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.114557 restraints weight = 3185.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.115098 restraints weight = 2973.497| |-----------------------------------------------------------------------------| r_work (final): 0.4149 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.132283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.123802 restraints weight = 10341.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.125555 restraints weight = 7638.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.126898 restraints weight = 5779.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.128036 restraints weight = 4433.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.128878 restraints weight = 3408.177| |-----------------------------------------------------------------------------| r_work (final): 0.4571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.138891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124642 restraints weight = 318.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124882 restraints weight = 261.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124882 restraints weight = 250.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124882 restraints weight = 250.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124882 restraints weight = 250.680| |-----------------------------------------------------------------------------| r_work (final): 0.3867 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.119342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114656 restraints weight = 617.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.114856 restraints weight = 573.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.115096 restraints weight = 539.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.115319 restraints weight = 504.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.115447 restraints weight = 480.018| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3076 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.961 22110 Z= 1.183 Angle : 2.201 41.893 30372 Z= 0.821 Chirality : 0.149 3.472 3882 Planarity : 0.009 0.163 3498 Dihedral : 6.700 30.482 2598 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.85 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.00 (0.16), residues: 2370 helix: -0.89 (0.25), residues: 384 sheet: -0.40 (0.18), residues: 792 loop : -2.16 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 503 TYR 0.038 0.003 TYR C 40 PHE 0.027 0.002 PHE H 227 TRP 0.022 0.002 TRP I 36 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01112 / 0.54 (21876) covalent geometry : angle 1.55483 / 0.64 (29718) SS BOND : bond 0.00837 / 0.61 ( 39) SS BOND : angle 2.48776 / 1.85 ( 78) hydrogen bonds : bond 0.05170 / 3.58 ( 696) hydrogen bonds : angle 6.66046 / 4.59 ( 1872) Misc. bond : bond 0.01605 / 0.82 ( 3) link_ALPHA1-2 : bond 0.23085 / 16.27 ( 12) link_ALPHA1-2 : angle 13.63609 / 11.09 ( 36) link_ALPHA1-3 : bond 0.42886 / 24.76 ( 21) link_ALPHA1-3 : angle 20.63938 / 13.46 ( 63) link_ALPHA1-6 : bond 0.54283 / 31.72 ( 18) link_ALPHA1-6 : angle 21.37231 / 16.87 ( 54) link_BETA1-4 : bond 0.01110 / 0.70 ( 81) link_BETA1-4 : angle 3.14818 / 2.26 ( 243) link_NAG-ASN : bond 0.01867 / 1.29 ( 60) link_NAG-ASN : angle 8.88275 / 5.69 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 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: 0.0009 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 : 0.001 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 27 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5510 (tmm) cc_final: -0.6355 (ttt) REVERT: D 475 MET cc_start: 0.6537 (mmp) cc_final: 0.5181 (tmm) REVERT: D 486 TYR cc_start: 0.6327 (m-80) cc_final: 0.5776 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0744 time to fit residues: 2.5947 Evaluate side-chains 18 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.143 Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.043 Fit side-chains REVERT: E 530 MET cc_start: 0.4010 (ptp) cc_final: 0.1184 (ptm) REVERT: E 586 TYR cc_start: 0.7295 (t80) cc_final: 0.7057 (t80) REVERT: E 587 LEU cc_start: 0.8688 (mm) cc_final: 0.8215 (mm) REVERT: E 590 GLN cc_start: 0.8043 (pt0) cc_final: 0.7515 (tm-30) REVERT: E 650 GLN cc_start: 0.8300 (tt0) cc_final: 0.7862 (pm20) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0889 time to fit residues: 2.0292 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.044 Evaluate side-chains 20 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.073 Fit side-chains REVERT: G 158 TYR cc_start: 0.4791 (t80) cc_final: 0.2419 (m-10) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0508 time to fit residues: 1.2827 Evaluate side-chains 15 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.064 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 : 0.002 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: 0.0017 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 136 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 0.0040 chunk 164 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 192 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 174 optimal weight: 0.4980 chunk 222 optimal weight: 0.0170 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 219 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.116278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111205 restraints weight = 1215.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112150 restraints weight = 866.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112633 restraints weight = 651.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.112967 restraints weight = 548.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.113247 restraints weight = 479.811| |-----------------------------------------------------------------------------| r_work (final): 0.3669 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.080317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.078731 restraints weight = 356.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.079526 restraints weight = 134.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.079960 restraints weight = 62.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.080114 restraints weight = 29.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.080198 restraints weight = 14.037| |-----------------------------------------------------------------------------| r_work (final): 0.3219 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078840 restraints weight = 469.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083318 restraints weight = 279.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084465 restraints weight = 230.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084465 restraints weight = 208.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084465 restraints weight = 208.330| |-----------------------------------------------------------------------------| r_work (final): 0.3018 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.125227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.110132 restraints weight = 20388.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.112005 restraints weight = 15663.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.113371 restraints weight = 12596.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.114410 restraints weight = 10511.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.115207 restraints weight = 9069.895| |-----------------------------------------------------------------------------| r_work (final): 0.4444 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103895 restraints weight = 5692.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.105898 restraints weight = 4268.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.107339 restraints weight = 3388.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108375 restraints weight = 2807.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.109085 restraints weight = 2433.631| |-----------------------------------------------------------------------------| r_work (final): 0.4035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.131830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.122174 restraints weight = 10935.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.124227 restraints weight = 8036.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.125724 restraints weight = 6059.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.126866 restraints weight = 4673.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.128080 restraints weight = 3697.025| |-----------------------------------------------------------------------------| r_work (final): 0.4576 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.141708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122954 restraints weight = 257.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123349 restraints weight = 227.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123348 restraints weight = 213.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123348 restraints weight = 213.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123348 restraints weight = 213.181| |-----------------------------------------------------------------------------| r_work (final): 0.3807 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.119446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114943 restraints weight = 630.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115166 restraints weight = 576.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115166 restraints weight = 539.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115164 restraints weight = 538.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115164 restraints weight = 538.784| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3074 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.958 22110 Z= 1.176 Angle : 2.187 41.815 30372 Z= 0.815 Chirality : 0.148 3.358 3882 Planarity : 0.013 0.359 3498 Dihedral : 6.878 43.427 2598 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.85 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.93 (0.16), residues: 2370 helix: -0.82 (0.25), residues: 384 sheet: -0.39 (0.18), residues: 792 loop : -2.10 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 327 TYR 0.030 0.003 TYR C 40 PHE 0.024 0.002 PHE G 227 TRP 0.037 0.003 TRP G 162 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.53 (21876) covalent geometry : angle 1.53913 / 0.63 (29718) SS BOND : bond 0.00922 / 0.64 ( 39) SS BOND : angle 2.63707 / 1.98 ( 78) hydrogen bonds : bond 0.04999 / 3.46 ( 696) hydrogen bonds : angle 6.56909 / 4.53 ( 1872) Misc. bond : bond 0.01711 / 0.87 ( 3) link_ALPHA1-2 : bond 0.23000 / 16.21 ( 12) link_ALPHA1-2 : angle 13.71640 / 11.16 ( 36) link_ALPHA1-3 : bond 0.42896 / 24.74 ( 21) link_ALPHA1-3 : angle 20.71620 / 13.50 ( 63) link_ALPHA1-6 : bond 0.54158 / 31.65 ( 18) link_ALPHA1-6 : angle 21.45582 / 16.95 ( 54) link_BETA1-4 : bond 0.01024 / 0.65 ( 81) link_BETA1-4 : angle 3.12775 / 2.25 ( 243) link_NAG-ASN : bond 0.01555 / 1.04 ( 60) link_NAG-ASN : angle 8.58675 / 5.46 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 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: 0.0009 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 : 0.001 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 26 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: -0.5396 (tmm) cc_final: -0.6214 (ttt) REVERT: D 475 MET cc_start: 0.6476 (mmp) cc_final: 0.5202 (tmm) REVERT: D 486 TYR cc_start: 0.6274 (m-80) cc_final: 0.5671 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0679 time to fit residues: 2.3386 Evaluate side-chains 18 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.158 Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.041 Fit side-chains REVERT: E 530 MET cc_start: 0.4763 (ptp) cc_final: 0.2085 (ptm) REVERT: E 586 TYR cc_start: 0.7867 (t80) cc_final: 0.7438 (t80) REVERT: E 587 LEU cc_start: 0.9341 (mm) cc_final: 0.9049 (mm) REVERT: E 590 GLN cc_start: 0.8550 (pt0) cc_final: 0.8154 (tm-30) REVERT: E 650 GLN cc_start: 0.8645 (tt0) cc_final: 0.8014 (pm20) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0629 time to fit residues: 1.3496 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.046 Evaluate side-chains 19 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.074 Fit side-chains REVERT: G 158 TYR cc_start: 0.4501 (t80) cc_final: 0.2361 (m-10) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0519 time to fit residues: 1.2362 Evaluate side-chains 15 residues out of total 193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.074 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 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: 0.0019 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: 237 random chunks: chunk 38 optimal weight: 0.0770 chunk 152 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 189 optimal weight: 0.0000 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 20 optimal weight: 0.2980 chunk 127 optimal weight: 0.0060 overall best weight: 0.0856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 301 ASN ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 219 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.115359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113068 restraints weight = 988.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113185 restraints weight = 910.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.113320 restraints weight = 830.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.113330 restraints weight = 746.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.113478 restraints weight = 739.950| |-----------------------------------------------------------------------------| r_work (final): 0.3699 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.079558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.077470 restraints weight = 352.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.078485 restraints weight = 131.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.078992 restraints weight = 62.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.079231 restraints weight = 30.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.079352 restraints weight = 14.814| |-----------------------------------------------------------------------------| r_work (final): 0.2900 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065593 restraints weight = 422.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067637 restraints weight = 345.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068517 restraints weight = 312.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068523 restraints weight = 302.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068523 restraints weight = 302.049| |-----------------------------------------------------------------------------| r_work (final): 0.2680 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.125845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.110409 restraints weight = 20205.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.112251 restraints weight = 15788.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.113546 restraints weight = 12661.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.114621 restraints weight = 10669.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.115439 restraints weight = 9185.982| |-----------------------------------------------------------------------------| r_work (final): 0.4427 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.127787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.104550 restraints weight = 5827.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.106470 restraints weight = 4340.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.107848 restraints weight = 3444.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.108908 restraints weight = 2880.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.109649 restraints weight = 2509.273| |-----------------------------------------------------------------------------| r_work (final): 0.4064 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.120168 restraints weight = 12253.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.122172 restraints weight = 9620.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.123740 restraints weight = 7762.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.125011 restraints weight = 6413.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.125952 restraints weight = 5340.901| |-----------------------------------------------------------------------------| r_work (final): 0.4535 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142843 restraints weight = 545.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144041 restraints weight = 339.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144693 restraints weight = 222.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145353 restraints weight = 163.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145667 restraints weight = 108.580| |-----------------------------------------------------------------------------| r_work (final): 0.3891 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104873 restraints weight = 3046.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104882 restraints weight = 3007.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104882 restraints weight = 2956.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104882 restraints weight = 2956.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104882 restraints weight = 2956.442| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3084 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.029 1.573 22110 Z= 1.431 Angle : 2.262 63.777 30372 Z= 0.830 Chirality : 0.209 6.450 3882 Planarity : 0.011 0.286 3498 Dihedral : 6.721 34.476 2598 Min Nonbonded Distance : 1.437 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.72 % Favored : 91.90 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2370 helix: -0.59 (0.25), residues: 402 sheet: -0.31 (0.18), residues: 774 loop : -2.21 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 327 TYR 0.019 0.002 TYR G 218 PHE 0.026 0.002 PHE I 227 TRP 0.027 0.003 TRP G 36 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.51 (21876) covalent geometry : angle 1.48760 / 0.61 (29718) SS BOND : bond 0.00774 / 0.53 ( 39) SS BOND : angle 2.41525 / 1.81 ( 78) hydrogen bonds : bond 0.04748 / 3.28 ( 696) hydrogen bonds : angle 6.43306 / 4.42 ( 1872) Misc. bond : bond 0.01633 / 0.83 ( 3) link_ALPHA1-2 : bond 0.22844 / 16.10 ( 12) link_ALPHA1-2 : angle 13.88450 / 11.31 ( 36) link_ALPHA1-3 : bond 0.42883 / 24.70 ( 21) link_ALPHA1-3 : angle 20.85848 / 13.57 ( 63) link_ALPHA1-6 : bond 0.53954 / 31.53 ( 18) link_ALPHA1-6 : angle 21.63971 / 17.12 ( 54) link_BETA1-4 : bond 0.00920 / 0.58 ( 81) link_BETA1-4 : angle 2.93683 / 2.13 ( 243) link_NAG-ASN : bond 0.31944 / 20.76 ( 60) link_NAG-ASN : angle 12.35515 / 7.40 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.86 seconds wall clock time: 46 minutes 16.24 seconds (2776.24 seconds total)