Starting phenix.real_space_refine on Thu Mar 5 08:28:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxn_23572/03_2026/7lxn_23572.cif" } resolution = 3.85 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= 0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12987 2.51 5 N 3351 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "I" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "E" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.32, per 1000 atoms: 0.26 Number of scatterers: 20820 At special positions: 0 Unit cell: (146.718, 155.952, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4368 8.00 N 3351 7.00 C 12987 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=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.12 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.13 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.12 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 7 " - " MAN G 8 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN a 7 " - " MAN a 8 " " MAN g 4 " - " MAN g 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN o 7 " - " MAN o 8 " " MAN u 4 " - " MAN u 5 " " MAN x 4 " - " MAN x 5 " " MAN x 5 " - " MAN x 6 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " " MAN x 7 " - " MAN x 8 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 5 " - " MAN G 6 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA a 3 " - " MAN a 4 " " MAN a 5 " - " MAN a 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA o 3 " - " MAN o 4 " " MAN o 5 " - " MAN o 6 " " BMA u 3 " - " MAN u 6 " " MAN u 6 " - " MAN u 7 " " BMA w 3 " - " MAN w 4 " " BMA x 3 " - " MAN x 7 " " MAN x 7 " - " MAN x 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " " 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 d 1 " - " NAG d 2 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 197 " " NAG 1 1 " - " ASN E 276 " " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 289 " " NAG C 602 " - " ASN C 392 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 392 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 138 " " NAG K 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 130 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN C 138 " " NAG b 1 " - " ASN C 88 " " NAG c 1 " - " ASN C 130 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 276 " " NAG o 1 " - " ASN E 138 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 130 " " NAG r 1 " - " ASN E 160 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 295 " " NAG w 1 " - " ASN E 301 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 448 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 732.2 milliseconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 22.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.791A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.710A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.908A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.792A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.160A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.790A pdb=" N GLY H 55 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.873A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.700A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.772A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 660 removed outlier: 3.512A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.127A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.810A pdb=" N GLY I 55 " --> pdb=" O HIS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.306A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.788A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.980A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.901A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 660 removed outlier: 4.567A pdb=" N SER F 644 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.875A pdb=" N GLY J 55 " --> pdb=" O HIS J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.349A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.016A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.002A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.721A 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: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 302 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.162A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.727A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.155A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR H 94 " --> pdb=" O ASP H 100Q" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.394A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.284A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.000A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.686A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.549A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 302 current: chain 'C' and resid 357 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 441 through 456 current: chain 'C' and resid 413 through 420 Processing sheet with id=AC7, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.146A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.824A pdb=" N TYR I 33 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.658A pdb=" N LYS I 96 " --> pdb=" O MET I 100P" (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET I 100P" --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY I 98 " --> pdb=" O PHE I 100N" (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE I 100N" --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG I 100 " --> pdb=" O THR I 100L" (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR I 100L" --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.460A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.364A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.002A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.982A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.667A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.547A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 441 through 456 current: chain 'E' and resid 413 through 420 Processing sheet with id=AE3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.121A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.746A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.190A pdb=" N CYS J 92 " --> pdb=" O TRP J 101 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP J 101 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR J 94 " --> pdb=" O ASP J 100Q" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.390A pdb=" N THR N 8 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE N 105 " --> pdb=" O THR N 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 19 through 23 738 hydrogen bonds defined for protein. 1890 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: 4.30 Time building geometry restraints manager: 3.02 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: 5147 1.32 - 1.46: 6949 1.46 - 1.60: 8990 1.60 - 1.74: 16 1.74 - 1.88: 132 Bond restraints: 21234 Sorted by residual: bond pdb=" CB HIS J 97 " pdb=" CG HIS J 97 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.91e+01 bond pdb=" CB THR E 37 " pdb=" OG1 THR E 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.70e+01 bond pdb=" CB THR C 37 " pdb=" OG1 THR C 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.64e+01 bond pdb=" CB HIS I 97 " pdb=" CG HIS I 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" CB HIS H 97 " pdb=" CG HIS H 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.60e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 23991 2.27 - 4.54: 4092 4.54 - 6.80: 672 6.80 - 9.07: 90 9.07 - 11.34: 21 Bond angle restraints: 28866 Sorted by residual: angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" N CYS E 73 " pdb=" CA CYS E 73 " pdb=" C CYS E 73 " ideal model delta sigma weight residual 114.56 104.56 10.00 1.27e+00 6.20e-01 6.20e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.11 -7.55 1.01e+00 9.80e-01 5.59e+01 angle pdb=" C VAL F 608 " pdb=" N PRO F 609 " pdb=" CA PRO F 609 " ideal model delta sigma weight residual 120.31 127.61 -7.30 9.80e-01 1.04e+00 5.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.05 -7.49 1.01e+00 9.80e-01 5.51e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 14087 22.15 - 44.31: 378 44.31 - 66.46: 122 66.46 - 88.62: 107 88.62 - 110.77: 72 Dihedral angle restraints: 14766 sinusoidal: 7890 harmonic: 6876 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -2.51 -83.49 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.45 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.50 63.50 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 14763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2556 0.108 - 0.216: 964 0.216 - 0.324: 168 0.324 - 0.431: 20 0.431 - 0.539: 15 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 MAN o 7 " pdb=" O3 BMA o 3 " pdb=" C2 MAN o 7 " pdb=" O5 MAN o 7 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.09e+02 chirality pdb=" C1 MAN G 7 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 MAN a 7 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 7 " pdb=" O5 MAN a 7 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 138 " 0.126 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN C 138 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN C 138 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 138 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 138 " 0.121 2.00e-02 2.50e+03 1.21e-01 1.84e+02 pdb=" CG ASN E 138 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN E 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN E 138 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.118 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN A 138 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.142 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4975 2.79 - 3.31: 18639 3.31 - 3.84: 35363 3.84 - 4.37: 41379 4.37 - 4.90: 66457 Nonbonded interactions: 166813 Sorted by model distance: nonbonded pdb=" O4 NAG m 2 " pdb=" O6 NAG m 2 " model vdw 2.257 3.040 nonbonded pdb=" O4 NAG Y 2 " pdb=" O6 NAG Y 2 " model vdw 2.258 3.040 nonbonded pdb=" O4 NAG 0 2 " pdb=" O6 NAG 0 2 " model vdw 2.259 3.040 nonbonded pdb=" O4 NAG B 701 " pdb=" O6 NAG B 701 " model vdw 2.262 3.040 nonbonded pdb=" O4 MAN S 7 " pdb=" O6 MAN S 7 " model vdw 2.272 3.040 ... (remaining 166808 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'S' and resid 4 through 7) selection = (chain 'V' and resid 6 through 9) selection = (chain 'a' and resid 5 through 8) selection = (chain 'g' and resid 4 through 7) selection = (chain 'j' and resid 6 through 9) selection = (chain 'o' and resid 5 through 8) selection = (chain 'u' and resid 4 through 7) selection = (chain 'x' and resid 6 through 9) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'k' selection = chain 'l' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.021 0.243 21432 Z= 1.135 Angle : 1.841 13.183 29421 Z= 1.120 Chirality : 0.112 0.539 3723 Planarity : 0.009 0.059 3429 Dihedral : 15.735 110.770 10203 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.29 % Favored : 98.58 % Rotamer: Outliers : 0.52 % Allowed : 0.43 % Favored : 99.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2325 helix: -0.69 (0.23), residues: 420 sheet: 1.20 (0.19), residues: 624 loop : 0.85 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 327 TYR 0.076 0.009 TYR C 40 PHE 0.037 0.007 PHE M 67C TRP 0.058 0.010 TRP E 112 HIS 0.011 0.002 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.02047 (21234) covalent geometry : angle 1.79442 (28866) SS BOND : bond 0.07179 ( 39) SS BOND : angle 2.76578 ( 78) hydrogen bonds : bond 0.16176 ( 702) hydrogen bonds : angle 7.50471 ( 1890) link_ALPHA1-2 : bond 0.06239 ( 12) link_ALPHA1-2 : angle 4.17493 ( 36) link_ALPHA1-3 : bond 0.05750 ( 15) link_ALPHA1-3 : angle 5.03185 ( 45) link_ALPHA1-6 : bond 0.06055 ( 21) link_ALPHA1-6 : angle 3.63329 ( 63) link_BETA1-4 : bond 0.05800 ( 60) link_BETA1-4 : angle 3.81358 ( 180) link_NAG-ASN : bond 0.07728 ( 51) link_NAG-ASN : angle 2.54064 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 545 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8750 (m-90) cc_final: 0.8457 (m-90) REVERT: A 100 MET cc_start: 0.7993 (mtp) cc_final: 0.7715 (mtm) REVERT: B 584 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 648 GLU cc_start: 0.8877 (tt0) cc_final: 0.8658 (tm-30) REVERT: H 100 MET cc_start: 0.8863 (mpp) cc_final: 0.8634 (mpp) REVERT: L 36 TYR cc_start: 0.8021 (m-80) cc_final: 0.7351 (m-80) REVERT: C 104 MET cc_start: 0.8807 (ttm) cc_final: 0.8472 (ttm) REVERT: C 202 THR cc_start: 0.9607 (m) cc_final: 0.9143 (p) REVERT: C 217 TYR cc_start: 0.8096 (m-80) cc_final: 0.7741 (m-10) REVERT: C 475 MET cc_start: 0.8339 (mmm) cc_final: 0.8032 (mmm) REVERT: D 624 ASP cc_start: 0.8440 (t70) cc_final: 0.8212 (m-30) REVERT: D 629 MET cc_start: 0.8300 (mmm) cc_final: 0.8053 (mmm) REVERT: D 648 GLU cc_start: 0.9042 (tt0) cc_final: 0.8718 (tm-30) REVERT: I 100 MET cc_start: 0.8871 (mpp) cc_final: 0.8650 (mpp) REVERT: M 21 ILE cc_start: 0.9167 (mt) cc_final: 0.8964 (mt) REVERT: E 104 MET cc_start: 0.8883 (ttm) cc_final: 0.8392 (ttm) REVERT: E 112 TRP cc_start: 0.8586 (m100) cc_final: 0.7987 (m100) REVERT: E 195 ASN cc_start: 0.8622 (m-40) cc_final: 0.8409 (t0) REVERT: E 283 THR cc_start: 0.8606 (m) cc_final: 0.8315 (p) REVERT: E 326 ILE cc_start: 0.9034 (mt) cc_final: 0.8817 (tt) REVERT: E 434 MET cc_start: 0.9124 (ttp) cc_final: 0.8594 (ttp) REVERT: F 584 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 648 GLU cc_start: 0.8811 (tt0) cc_final: 0.8091 (tm-30) outliers start: 11 outliers final: 9 residues processed: 556 average time/residue: 0.1624 time to fit residues: 134.1361 Evaluate side-chains 278 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 607 ASN B 650 GLN C 229 ASN C 362 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN I 39 GLN I 68 HIS E 195 ASN E 229 ASN E 362 ASN F 591 GLN F 625 ASN J 68 HIS N 95CASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.077884 restraints weight = 63257.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080744 restraints weight = 34646.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082568 restraints weight = 24861.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083649 restraints weight = 20448.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084195 restraints weight = 18259.524| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21432 Z= 0.253 Angle : 0.932 15.708 29421 Z= 0.439 Chirality : 0.055 0.448 3723 Planarity : 0.005 0.047 3429 Dihedral : 13.237 88.899 5763 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.80 % Allowed : 8.40 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2325 helix: 0.48 (0.26), residues: 405 sheet: 0.91 (0.19), residues: 615 loop : 0.43 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 579 TYR 0.019 0.002 TYR J 33 PHE 0.030 0.002 PHE C 233 TRP 0.022 0.003 TRP E 112 HIS 0.008 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00555 (21234) covalent geometry : angle 0.86337 (28866) SS BOND : bond 0.00550 ( 39) SS BOND : angle 1.26721 ( 78) hydrogen bonds : bond 0.05959 ( 702) hydrogen bonds : angle 6.00916 ( 1890) link_ALPHA1-2 : bond 0.00788 ( 12) link_ALPHA1-2 : angle 2.39061 ( 36) link_ALPHA1-3 : bond 0.01338 ( 15) link_ALPHA1-3 : angle 2.11393 ( 45) link_ALPHA1-6 : bond 0.00515 ( 21) link_ALPHA1-6 : angle 1.85563 ( 63) link_BETA1-4 : bond 0.00713 ( 60) link_BETA1-4 : angle 2.86337 ( 180) link_NAG-ASN : bond 0.00699 ( 51) link_NAG-ASN : angle 3.41894 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8606 (m-90) cc_final: 0.8245 (m-90) REVERT: A 475 MET cc_start: 0.8215 (mmm) cc_final: 0.7601 (tpp) REVERT: B 581 LEU cc_start: 0.9467 (tp) cc_final: 0.9052 (tt) REVERT: B 584 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8523 (mp0) REVERT: B 623 TRP cc_start: 0.7258 (m100) cc_final: 0.6948 (m-10) REVERT: B 648 GLU cc_start: 0.8729 (tt0) cc_final: 0.8488 (tm-30) REVERT: H 16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7128 (tt0) REVERT: H 100 MET cc_start: 0.8786 (mpp) cc_final: 0.8525 (mmt) REVERT: L 28 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8227 (mm) REVERT: L 36 TYR cc_start: 0.8450 (m-80) cc_final: 0.7707 (m-80) REVERT: L 78 VAL cc_start: 0.9217 (t) cc_final: 0.8895 (m) REVERT: L 95 ASN cc_start: 0.8609 (m-40) cc_final: 0.8386 (m-40) REVERT: C 104 MET cc_start: 0.8469 (ttm) cc_final: 0.8232 (ttm) REVERT: C 202 THR cc_start: 0.9563 (m) cc_final: 0.9276 (p) REVERT: C 260 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8427 (mm) REVERT: C 475 MET cc_start: 0.8215 (mmm) cc_final: 0.7700 (mmm) REVERT: D 545 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6376 (mm) REVERT: D 577 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8673 (tm-30) REVERT: D 584 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 630 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8292 (mm-30) REVERT: D 648 GLU cc_start: 0.8911 (tt0) cc_final: 0.8639 (tm-30) REVERT: I 16 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7069 (tt0) REVERT: I 22 CYS cc_start: 0.1289 (t) cc_final: 0.0496 (t) REVERT: M 36 TYR cc_start: 0.8546 (m-80) cc_final: 0.8255 (m-80) REVERT: M 50 ASN cc_start: 0.8955 (t0) cc_final: 0.8702 (t0) REVERT: M 78 VAL cc_start: 0.9421 (t) cc_final: 0.9098 (m) REVERT: M 95 ASN cc_start: 0.8466 (m-40) cc_final: 0.8236 (m-40) REVERT: E 159 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: E 283 THR cc_start: 0.8572 (m) cc_final: 0.8185 (p) REVERT: E 475 MET cc_start: 0.8148 (tpp) cc_final: 0.7589 (tpp) REVERT: F 584 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8492 (mt-10) REVERT: F 626 MET cc_start: 0.7827 (ttt) cc_final: 0.7536 (ttt) REVERT: F 648 GLU cc_start: 0.8502 (tt0) cc_final: 0.8238 (tm-30) REVERT: J 16 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6999 (tt0) REVERT: N 79 GLU cc_start: 0.8123 (mp0) cc_final: 0.7884 (mp0) REVERT: N 103 THR cc_start: 0.8138 (m) cc_final: 0.7547 (p) outliers start: 59 outliers final: 39 residues processed: 356 average time/residue: 0.1419 time to fit residues: 78.4787 Evaluate side-chains 283 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN H 97 HIS L 52 ASN C 72 HIS ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS M 52 ASN E 72 HIS F 625 ASN N 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.096770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074796 restraints weight = 64308.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.077571 restraints weight = 35682.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079293 restraints weight = 25753.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080261 restraints weight = 21325.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080880 restraints weight = 19173.633| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21432 Z= 0.261 Angle : 0.859 12.673 29421 Z= 0.407 Chirality : 0.054 0.564 3723 Planarity : 0.005 0.084 3429 Dihedral : 11.468 88.322 5763 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.61 % Allowed : 10.54 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2325 helix: 0.23 (0.26), residues: 405 sheet: 0.77 (0.19), residues: 657 loop : 0.09 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 99 TYR 0.028 0.002 TYR H 33 PHE 0.021 0.002 PHE C 233 TRP 0.021 0.002 TRP M 91 HIS 0.024 0.002 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00582 (21234) covalent geometry : angle 0.79914 (28866) SS BOND : bond 0.00652 ( 39) SS BOND : angle 1.22048 ( 78) hydrogen bonds : bond 0.05109 ( 702) hydrogen bonds : angle 5.71398 ( 1890) link_ALPHA1-2 : bond 0.00708 ( 12) link_ALPHA1-2 : angle 2.86392 ( 36) link_ALPHA1-3 : bond 0.01554 ( 15) link_ALPHA1-3 : angle 2.41431 ( 45) link_ALPHA1-6 : bond 0.00462 ( 21) link_ALPHA1-6 : angle 1.65710 ( 63) link_BETA1-4 : bond 0.00741 ( 60) link_BETA1-4 : angle 2.48802 ( 180) link_NAG-ASN : bond 0.00589 ( 51) link_NAG-ASN : angle 2.93983 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 238 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8712 (m-90) cc_final: 0.8388 (m-90) REVERT: A 202 THR cc_start: 0.9592 (m) cc_final: 0.9265 (p) REVERT: A 475 MET cc_start: 0.8188 (mmm) cc_final: 0.7485 (tpp) REVERT: A 479 TRP cc_start: 0.8347 (m-90) cc_final: 0.8109 (m-90) REVERT: B 577 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8587 (tm-30) REVERT: B 623 TRP cc_start: 0.7157 (m-10) cc_final: 0.6800 (m-10) REVERT: B 642 ILE cc_start: 0.9509 (mt) cc_final: 0.9289 (mm) REVERT: B 643 TYR cc_start: 0.8879 (m-10) cc_final: 0.8663 (m-10) REVERT: B 647 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8652 (mt-10) REVERT: H 100 MET cc_start: 0.8790 (mpp) cc_final: 0.8469 (mmt) REVERT: L 83 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 104 MET cc_start: 0.8740 (ttm) cc_final: 0.8529 (ttm) REVERT: C 475 MET cc_start: 0.8151 (mmm) cc_final: 0.7902 (mmm) REVERT: D 577 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8650 (tm-30) REVERT: D 581 LEU cc_start: 0.9464 (tp) cc_final: 0.9213 (tt) REVERT: D 584 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8396 (mt-10) REVERT: D 626 MET cc_start: 0.8089 (tpp) cc_final: 0.7652 (tpp) REVERT: D 630 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 648 GLU cc_start: 0.8795 (tt0) cc_final: 0.8570 (tm-30) REVERT: I 105 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7923 (p) REVERT: M 83 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7610 (tm-30) REVERT: M 85 ASP cc_start: 0.7029 (m-30) cc_final: 0.6819 (m-30) REVERT: E 159 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: E 260 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 475 MET cc_start: 0.8208 (tpp) cc_final: 0.7854 (tpp) REVERT: F 629 MET cc_start: 0.9125 (mmm) cc_final: 0.8716 (mmt) REVERT: N 79 GLU cc_start: 0.8384 (mp0) cc_final: 0.8067 (mp0) outliers start: 76 outliers final: 53 residues processed: 290 average time/residue: 0.1369 time to fit residues: 62.3006 Evaluate side-chains 251 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 50 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS D 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.099075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.078960 restraints weight = 63436.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080486 restraints weight = 39360.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081335 restraints weight = 30493.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081823 restraints weight = 26409.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082244 restraints weight = 24314.864| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21432 Z= 0.157 Angle : 0.746 9.805 29421 Z= 0.347 Chirality : 0.050 0.483 3723 Planarity : 0.004 0.046 3429 Dihedral : 10.280 81.834 5763 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.61 % Allowed : 11.92 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2325 helix: 0.62 (0.27), residues: 393 sheet: 0.74 (0.19), residues: 672 loop : 0.11 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 20 TYR 0.035 0.002 TYR F 643 PHE 0.017 0.001 PHE C 233 TRP 0.013 0.001 TRP B 631 HIS 0.020 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00345 (21234) covalent geometry : angle 0.69004 (28866) SS BOND : bond 0.00401 ( 39) SS BOND : angle 0.98468 ( 78) hydrogen bonds : bond 0.04400 ( 702) hydrogen bonds : angle 5.40155 ( 1890) link_ALPHA1-2 : bond 0.00575 ( 12) link_ALPHA1-2 : angle 2.61272 ( 36) link_ALPHA1-3 : bond 0.01602 ( 15) link_ALPHA1-3 : angle 2.10222 ( 45) link_ALPHA1-6 : bond 0.00614 ( 21) link_ALPHA1-6 : angle 1.53391 ( 63) link_BETA1-4 : bond 0.00682 ( 60) link_BETA1-4 : angle 2.30646 ( 180) link_NAG-ASN : bond 0.00462 ( 51) link_NAG-ASN : angle 2.58170 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8697 (m-90) cc_final: 0.8328 (m-90) REVERT: A 202 THR cc_start: 0.9561 (m) cc_final: 0.9185 (p) REVERT: A 475 MET cc_start: 0.8078 (mmm) cc_final: 0.6548 (tpp) REVERT: A 479 TRP cc_start: 0.8276 (m-90) cc_final: 0.7796 (m-90) REVERT: B 577 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 623 TRP cc_start: 0.7134 (m-10) cc_final: 0.6797 (m-10) REVERT: B 642 ILE cc_start: 0.9532 (mt) cc_final: 0.9291 (mm) REVERT: B 643 TYR cc_start: 0.8919 (m-10) cc_final: 0.8710 (m-10) REVERT: L 83 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7778 (pp20) REVERT: D 577 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8550 (tm-30) REVERT: D 584 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8328 (mt-10) REVERT: D 648 GLU cc_start: 0.8737 (tt0) cc_final: 0.8454 (tm-30) REVERT: I 105 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7744 (p) REVERT: M 83 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7720 (pp20) REVERT: M 85 ASP cc_start: 0.6961 (m-30) cc_final: 0.6672 (m-30) REVERT: E 159 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: E 260 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8703 (mm) REVERT: F 577 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8302 (tm-30) REVERT: F 584 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7836 (mp0) REVERT: N 79 GLU cc_start: 0.8471 (mp0) cc_final: 0.8209 (mp0) outliers start: 55 outliers final: 38 residues processed: 269 average time/residue: 0.1431 time to fit residues: 59.6352 Evaluate side-chains 247 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076409 restraints weight = 64734.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079075 restraints weight = 36208.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080783 restraints weight = 26319.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081817 restraints weight = 21772.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082366 restraints weight = 19478.611| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21432 Z= 0.273 Angle : 0.841 11.188 29421 Z= 0.393 Chirality : 0.052 0.544 3723 Planarity : 0.005 0.103 3429 Dihedral : 10.431 87.214 5761 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.99 % Allowed : 10.73 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2325 helix: 0.40 (0.27), residues: 393 sheet: 0.73 (0.20), residues: 642 loop : -0.20 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 30 TYR 0.046 0.003 TYR F 643 PHE 0.020 0.002 PHE N 98 TRP 0.018 0.002 TRP M 91 HIS 0.008 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00618 (21234) covalent geometry : angle 0.78532 (28866) SS BOND : bond 0.00680 ( 39) SS BOND : angle 1.32875 ( 78) hydrogen bonds : bond 0.04760 ( 702) hydrogen bonds : angle 5.58676 ( 1890) link_ALPHA1-2 : bond 0.00403 ( 12) link_ALPHA1-2 : angle 2.84835 ( 36) link_ALPHA1-3 : bond 0.01469 ( 15) link_ALPHA1-3 : angle 2.40653 ( 45) link_ALPHA1-6 : bond 0.00435 ( 21) link_ALPHA1-6 : angle 1.72536 ( 63) link_BETA1-4 : bond 0.00694 ( 60) link_BETA1-4 : angle 2.33323 ( 180) link_NAG-ASN : bond 0.00660 ( 51) link_NAG-ASN : angle 2.73249 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 203 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8724 (m-90) cc_final: 0.8428 (m-10) REVERT: A 202 THR cc_start: 0.9599 (m) cc_final: 0.9180 (p) REVERT: A 475 MET cc_start: 0.8158 (mmm) cc_final: 0.7349 (tpp) REVERT: A 479 TRP cc_start: 0.8388 (m-90) cc_final: 0.8121 (m-90) REVERT: B 577 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 642 ILE cc_start: 0.9503 (mt) cc_final: 0.9302 (mm) REVERT: L 28 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8441 (mm) REVERT: L 105 ILE cc_start: 0.8853 (mt) cc_final: 0.8633 (pt) REVERT: C 159 PHE cc_start: 0.8389 (m-10) cc_final: 0.8188 (m-80) REVERT: C 201 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8543 (tt) REVERT: D 577 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8584 (tm-30) REVERT: D 584 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 621 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: D 630 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7941 (mm-30) REVERT: D 648 GLU cc_start: 0.8776 (tt0) cc_final: 0.8562 (tm-30) REVERT: M 83 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7710 (pp20) REVERT: E 159 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: E 260 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (mm) REVERT: E 475 MET cc_start: 0.8275 (tpp) cc_final: 0.8046 (tpp) REVERT: F 577 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 581 LEU cc_start: 0.9424 (tp) cc_final: 0.9216 (tp) REVERT: F 584 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7933 (mt-10) REVERT: F 629 MET cc_start: 0.9178 (mmm) cc_final: 0.8836 (mmt) REVERT: N 79 GLU cc_start: 0.8611 (mp0) cc_final: 0.8296 (mp0) outliers start: 84 outliers final: 59 residues processed: 266 average time/residue: 0.1439 time to fit residues: 59.6982 Evaluate side-chains 249 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN E 425 ASN J 5 GLN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.099688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077584 restraints weight = 64433.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080349 restraints weight = 36348.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082072 restraints weight = 26392.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083100 restraints weight = 21940.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083757 restraints weight = 19675.820| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21432 Z= 0.187 Angle : 0.769 11.741 29421 Z= 0.358 Chirality : 0.050 0.477 3723 Planarity : 0.004 0.051 3429 Dihedral : 10.040 82.979 5761 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.37 % Allowed : 12.06 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2325 helix: 0.48 (0.27), residues: 393 sheet: 0.65 (0.20), residues: 642 loop : -0.13 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 20 TYR 0.038 0.002 TYR F 643 PHE 0.015 0.001 PHE C 233 TRP 0.013 0.001 TRP B 631 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00419 (21234) covalent geometry : angle 0.71346 (28866) SS BOND : bond 0.00533 ( 39) SS BOND : angle 1.75707 ( 78) hydrogen bonds : bond 0.04216 ( 702) hydrogen bonds : angle 5.40814 ( 1890) link_ALPHA1-2 : bond 0.00378 ( 12) link_ALPHA1-2 : angle 2.66506 ( 36) link_ALPHA1-3 : bond 0.01665 ( 15) link_ALPHA1-3 : angle 2.17700 ( 45) link_ALPHA1-6 : bond 0.00585 ( 21) link_ALPHA1-6 : angle 1.53892 ( 63) link_BETA1-4 : bond 0.00682 ( 60) link_BETA1-4 : angle 2.21037 ( 180) link_NAG-ASN : bond 0.00573 ( 51) link_NAG-ASN : angle 2.54089 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 208 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8775 (m-90) cc_final: 0.8395 (m-10) REVERT: A 475 MET cc_start: 0.8049 (mmm) cc_final: 0.6709 (tpp) REVERT: A 479 TRP cc_start: 0.8333 (m-90) cc_final: 0.7903 (m-90) REVERT: B 577 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 584 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7685 (mp0) REVERT: B 626 MET cc_start: 0.8369 (tpp) cc_final: 0.7932 (tpp) REVERT: L 105 ILE cc_start: 0.8837 (mt) cc_final: 0.8624 (pt) REVERT: C 326 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8306 (tt) REVERT: C 475 MET cc_start: 0.8166 (mmm) cc_final: 0.7660 (tmm) REVERT: D 575 GLN cc_start: 0.8872 (tp40) cc_final: 0.8656 (tp40) REVERT: D 577 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8505 (tm-30) REVERT: D 584 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8307 (mt-10) REVERT: D 648 GLU cc_start: 0.8739 (tt0) cc_final: 0.8486 (tm-30) REVERT: M 83 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7509 (pp20) REVERT: E 260 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (mm) REVERT: F 577 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8426 (tm-30) REVERT: F 584 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 629 MET cc_start: 0.9137 (mmm) cc_final: 0.8841 (mmt) REVERT: N 79 GLU cc_start: 0.8643 (mp0) cc_final: 0.8404 (mp0) outliers start: 71 outliers final: 53 residues processed: 261 average time/residue: 0.1482 time to fit residues: 60.5633 Evaluate side-chains 240 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.096980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.077433 restraints weight = 63426.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.078838 restraints weight = 39673.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079481 restraints weight = 32669.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079869 restraints weight = 28166.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080225 restraints weight = 26122.907| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21432 Z= 0.181 Angle : 0.758 11.251 29421 Z= 0.352 Chirality : 0.049 0.468 3723 Planarity : 0.004 0.052 3429 Dihedral : 9.853 81.623 5761 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.37 % Allowed : 12.20 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2325 helix: 0.50 (0.27), residues: 393 sheet: 0.49 (0.20), residues: 663 loop : -0.07 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.023 0.002 TYR D 586 PHE 0.014 0.002 PHE C 233 TRP 0.017 0.001 TRP B 631 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00406 (21234) covalent geometry : angle 0.70432 (28866) SS BOND : bond 0.00740 ( 39) SS BOND : angle 1.63461 ( 78) hydrogen bonds : bond 0.04127 ( 702) hydrogen bonds : angle 5.31687 ( 1890) link_ALPHA1-2 : bond 0.00346 ( 12) link_ALPHA1-2 : angle 2.60627 ( 36) link_ALPHA1-3 : bond 0.01577 ( 15) link_ALPHA1-3 : angle 2.20230 ( 45) link_ALPHA1-6 : bond 0.00575 ( 21) link_ALPHA1-6 : angle 1.55793 ( 63) link_BETA1-4 : bond 0.00643 ( 60) link_BETA1-4 : angle 2.11988 ( 180) link_NAG-ASN : bond 0.00469 ( 51) link_NAG-ASN : angle 2.46578 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7999 (mmm) cc_final: 0.6671 (tpp) REVERT: A 479 TRP cc_start: 0.8282 (m-90) cc_final: 0.7867 (m-90) REVERT: B 577 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 584 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 626 MET cc_start: 0.7997 (tpp) cc_final: 0.7786 (tpp) REVERT: L 28 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 326 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8225 (tt) REVERT: C 475 MET cc_start: 0.8187 (mmm) cc_final: 0.7731 (tmm) REVERT: D 575 GLN cc_start: 0.8865 (tp40) cc_final: 0.8641 (tp40) REVERT: D 577 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 584 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 586 TYR cc_start: 0.9068 (t80) cc_final: 0.8678 (t80) REVERT: D 648 GLU cc_start: 0.8716 (tt0) cc_final: 0.8503 (tm-30) REVERT: M 83 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7665 (pp20) REVERT: E 159 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: E 260 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8850 (mm) REVERT: F 577 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8402 (tm-30) REVERT: F 584 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8025 (mt-10) REVERT: F 629 MET cc_start: 0.9153 (mmm) cc_final: 0.8887 (mmt) REVERT: N 79 GLU cc_start: 0.8557 (mp0) cc_final: 0.8308 (mp0) REVERT: N 83 GLU cc_start: 0.8146 (pp20) cc_final: 0.7608 (pp20) outliers start: 71 outliers final: 56 residues processed: 241 average time/residue: 0.1507 time to fit residues: 56.8514 Evaluate side-chains 240 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.096247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.076508 restraints weight = 63291.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.077986 restraints weight = 40463.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078253 restraints weight = 33300.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078857 restraints weight = 29507.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079054 restraints weight = 26964.316| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21432 Z= 0.204 Angle : 0.771 10.656 29421 Z= 0.359 Chirality : 0.049 0.462 3723 Planarity : 0.004 0.052 3429 Dihedral : 9.863 81.980 5761 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.66 % Allowed : 12.25 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2325 helix: 0.50 (0.27), residues: 393 sheet: 0.41 (0.20), residues: 663 loop : -0.15 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.021 0.002 TYR H 33 PHE 0.012 0.002 PHE C 233 TRP 0.015 0.002 TRP B 631 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00463 (21234) covalent geometry : angle 0.71803 (28866) SS BOND : bond 0.00597 ( 39) SS BOND : angle 1.58394 ( 78) hydrogen bonds : bond 0.04135 ( 702) hydrogen bonds : angle 5.33995 ( 1890) link_ALPHA1-2 : bond 0.00311 ( 12) link_ALPHA1-2 : angle 2.62183 ( 36) link_ALPHA1-3 : bond 0.01602 ( 15) link_ALPHA1-3 : angle 2.23937 ( 45) link_ALPHA1-6 : bond 0.00556 ( 21) link_ALPHA1-6 : angle 1.58366 ( 63) link_BETA1-4 : bond 0.00635 ( 60) link_BETA1-4 : angle 2.11276 ( 180) link_NAG-ASN : bond 0.00500 ( 51) link_NAG-ASN : angle 2.49772 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 182 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7971 (mmm) cc_final: 0.6727 (tpp) REVERT: A 479 TRP cc_start: 0.8313 (m-90) cc_final: 0.7874 (m-90) REVERT: B 530 MET cc_start: 0.7842 (mpp) cc_final: 0.7035 (mpp) REVERT: B 577 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 584 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 626 MET cc_start: 0.8003 (tpp) cc_final: 0.7361 (tpp) REVERT: L 9 PHE cc_start: 0.7991 (m-80) cc_final: 0.7559 (m-10) REVERT: L 28 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8389 (mm) REVERT: C 159 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: C 326 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8235 (tt) REVERT: C 475 MET cc_start: 0.8222 (mmm) cc_final: 0.7788 (tmm) REVERT: D 575 GLN cc_start: 0.8866 (tp40) cc_final: 0.8666 (tp40) REVERT: D 577 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8481 (tm-30) REVERT: D 584 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8291 (mt-10) REVERT: D 630 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7704 (tp30) REVERT: D 649 SER cc_start: 0.9150 (m) cc_final: 0.8557 (p) REVERT: M 83 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7716 (pp20) REVERT: E 159 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: E 283 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8401 (p) REVERT: F 577 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8413 (tm-30) REVERT: F 584 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8016 (mt-10) REVERT: F 629 MET cc_start: 0.9134 (mmm) cc_final: 0.8768 (mmm) REVERT: J 28 LEU cc_start: 0.8971 (mm) cc_final: 0.8770 (tt) REVERT: N 79 GLU cc_start: 0.8578 (mp0) cc_final: 0.8334 (mp0) REVERT: N 83 GLU cc_start: 0.8150 (pp20) cc_final: 0.7669 (pp20) REVERT: N 88 CYS cc_start: 0.6478 (p) cc_final: 0.6198 (p) outliers start: 77 outliers final: 59 residues processed: 240 average time/residue: 0.1460 time to fit residues: 55.4063 Evaluate side-chains 241 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 94 optimal weight: 0.0000 chunk 67 optimal weight: 0.9990 overall best weight: 2.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.097441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077900 restraints weight = 63204.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079407 restraints weight = 39412.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079795 restraints weight = 32871.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080175 restraints weight = 29160.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080862 restraints weight = 26529.072| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21432 Z= 0.153 Angle : 0.729 10.041 29421 Z= 0.337 Chirality : 0.048 0.435 3723 Planarity : 0.004 0.052 3429 Dihedral : 9.528 77.966 5761 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.23 % Allowed : 12.73 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2325 helix: 0.62 (0.27), residues: 390 sheet: 0.36 (0.19), residues: 669 loop : -0.02 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.027 0.002 TYR D 586 PHE 0.014 0.001 PHE C 233 TRP 0.022 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00340 (21234) covalent geometry : angle 0.67940 (28866) SS BOND : bond 0.00539 ( 39) SS BOND : angle 1.42749 ( 78) hydrogen bonds : bond 0.03858 ( 702) hydrogen bonds : angle 5.13480 ( 1890) link_ALPHA1-2 : bond 0.00356 ( 12) link_ALPHA1-2 : angle 2.51463 ( 36) link_ALPHA1-3 : bond 0.01682 ( 15) link_ALPHA1-3 : angle 2.14328 ( 45) link_ALPHA1-6 : bond 0.00650 ( 21) link_ALPHA1-6 : angle 1.51173 ( 63) link_BETA1-4 : bond 0.00626 ( 60) link_BETA1-4 : angle 2.02656 ( 180) link_NAG-ASN : bond 0.00383 ( 51) link_NAG-ASN : angle 2.35488 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8836 (m-10) cc_final: 0.8450 (m-10) REVERT: A 475 MET cc_start: 0.7862 (mmm) cc_final: 0.6447 (tpp) REVERT: A 479 TRP cc_start: 0.8238 (m-90) cc_final: 0.7800 (m-90) REVERT: B 577 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 584 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 626 MET cc_start: 0.8025 (tpp) cc_final: 0.7787 (tpp) REVERT: L 9 PHE cc_start: 0.7979 (m-80) cc_final: 0.7530 (m-10) REVERT: C 159 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: C 326 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 475 MET cc_start: 0.8144 (mmm) cc_final: 0.7737 (tmm) REVERT: D 575 GLN cc_start: 0.8815 (tp40) cc_final: 0.8588 (tp40) REVERT: D 577 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 584 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8284 (mt-10) REVERT: M 83 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7772 (pp20) REVERT: E 159 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: E 283 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8380 (p) REVERT: F 577 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8356 (tm-30) REVERT: F 584 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7984 (mt-10) REVERT: N 79 GLU cc_start: 0.8567 (mp0) cc_final: 0.8315 (mp0) REVERT: N 83 GLU cc_start: 0.8161 (pp20) cc_final: 0.7669 (pp20) REVERT: N 88 CYS cc_start: 0.6386 (p) cc_final: 0.6131 (p) outliers start: 68 outliers final: 58 residues processed: 242 average time/residue: 0.1405 time to fit residues: 53.9427 Evaluate side-chains 243 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 141 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076499 restraints weight = 65078.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079169 restraints weight = 36312.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080817 restraints weight = 26262.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081809 restraints weight = 21808.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.082427 restraints weight = 19579.506| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21432 Z= 0.228 Angle : 0.791 10.185 29421 Z= 0.369 Chirality : 0.050 0.461 3723 Planarity : 0.005 0.053 3429 Dihedral : 9.801 81.141 5761 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.28 % Allowed : 12.96 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2325 helix: 0.63 (0.28), residues: 387 sheet: 0.45 (0.20), residues: 621 loop : -0.17 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.038 0.002 TYR B 643 PHE 0.012 0.002 PHE N 98 TRP 0.014 0.002 TRP B 631 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00521 (21234) covalent geometry : angle 0.74093 (28866) SS BOND : bond 0.00645 ( 39) SS BOND : angle 1.50238 ( 78) hydrogen bonds : bond 0.04208 ( 702) hydrogen bonds : angle 5.30013 ( 1890) link_ALPHA1-2 : bond 0.00317 ( 12) link_ALPHA1-2 : angle 2.61555 ( 36) link_ALPHA1-3 : bond 0.01585 ( 15) link_ALPHA1-3 : angle 2.27672 ( 45) link_ALPHA1-6 : bond 0.00550 ( 21) link_ALPHA1-6 : angle 1.62138 ( 63) link_BETA1-4 : bond 0.00655 ( 60) link_BETA1-4 : angle 2.09965 ( 180) link_NAG-ASN : bond 0.00521 ( 51) link_NAG-ASN : angle 2.50407 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8868 (m-10) cc_final: 0.8556 (m-10) REVERT: A 475 MET cc_start: 0.7958 (mmm) cc_final: 0.6973 (tpp) REVERT: A 479 TRP cc_start: 0.8328 (m-90) cc_final: 0.8000 (m-90) REVERT: B 577 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 584 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8007 (mt-10) REVERT: H 100 MET cc_start: 0.8613 (mpp) cc_final: 0.8312 (mpp) REVERT: L 9 PHE cc_start: 0.7875 (m-80) cc_final: 0.7470 (m-10) REVERT: C 159 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: C 326 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8207 (tt) REVERT: C 475 MET cc_start: 0.8246 (mmm) cc_final: 0.7855 (tmm) REVERT: D 575 GLN cc_start: 0.8833 (tp40) cc_final: 0.8607 (tp40) REVERT: D 577 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 584 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8313 (mt-10) REVERT: D 630 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7790 (tp30) REVERT: M 83 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7722 (pp20) REVERT: E 159 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: E 283 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8406 (p) REVERT: F 577 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8400 (tm-30) REVERT: F 584 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7996 (mt-10) REVERT: N 79 GLU cc_start: 0.8651 (mp0) cc_final: 0.8392 (mp0) REVERT: N 83 GLU cc_start: 0.8094 (pp20) cc_final: 0.7580 (pp20) outliers start: 69 outliers final: 60 residues processed: 229 average time/residue: 0.1444 time to fit residues: 52.6628 Evaluate side-chains 235 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 644 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 111 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.096803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.077213 restraints weight = 63397.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078837 restraints weight = 39708.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079144 restraints weight = 32878.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079542 restraints weight = 29209.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.079988 restraints weight = 26630.490| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21432 Z= 0.178 Angle : 0.755 10.206 29421 Z= 0.350 Chirality : 0.049 0.443 3723 Planarity : 0.004 0.053 3429 Dihedral : 9.607 78.624 5761 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.13 % Allowed : 12.96 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2325 helix: 0.61 (0.27), residues: 387 sheet: 0.34 (0.20), residues: 633 loop : -0.12 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.021 0.002 TYR B 643 PHE 0.013 0.001 PHE C 233 TRP 0.024 0.001 TRP C 69 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00405 (21234) covalent geometry : angle 0.70534 (28866) SS BOND : bond 0.00553 ( 39) SS BOND : angle 1.51590 ( 78) hydrogen bonds : bond 0.04007 ( 702) hydrogen bonds : angle 5.19557 ( 1890) link_ALPHA1-2 : bond 0.00336 ( 12) link_ALPHA1-2 : angle 2.53138 ( 36) link_ALPHA1-3 : bond 0.01652 ( 15) link_ALPHA1-3 : angle 2.18764 ( 45) link_ALPHA1-6 : bond 0.00627 ( 21) link_ALPHA1-6 : angle 1.53639 ( 63) link_BETA1-4 : bond 0.00622 ( 60) link_BETA1-4 : angle 2.02576 ( 180) link_NAG-ASN : bond 0.00416 ( 51) link_NAG-ASN : angle 2.39834 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.91 seconds wall clock time: 53 minutes 56.59 seconds (3236.59 seconds total)