Starting phenix.real_space_refine on Thu Mar 5 08:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxm_23571/03_2026/7lxm_23571.cif" } resolution = 3.41 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= 0.014 sd= 0.103 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 73 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: "N" 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: "P" 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: "O" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 4.98, per 1000 atoms: 0.24 Number of scatterers: 20820 At special positions: 0 Unit cell: (149.796, 154.926, 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=2.15 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=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.18 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 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=2.15 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=2.05 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=2.16 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=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 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=2.07 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 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: 2.47 Conformation dependent library (CDL) restraints added in 886.0 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: 59 helices and 45 sheets defined 21.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.184A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.725A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.937A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.834A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.140A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.242A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.887A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.958A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.214A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (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 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.645A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.899A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.841A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.133A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.354A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 660 removed outlier: 3.605A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.143A pdb=" N ASN N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 65 No H-bonds generated for 'chain 'N' and resid 63 through 65' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 3.636A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.903A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.770A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.144A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.502A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 Processing helix chain 'F' and resid 651 through 660 removed outlier: 3.607A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.173A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.082A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.792A 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: 4.641A 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 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: 6.658A 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: 6.631A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.588A 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: 10.588A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.862A 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: 6.198A 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: 6.568A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.754A 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: 7.127A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.018A 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: 6.446A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.748A 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: 4.750A 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: 4.668A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 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: 6.735A 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: 6.634A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (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: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (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 308 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.499A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.127A pdb=" N CYS N 92 " --> pdb=" O TRP N 101 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP N 101 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR N 94 " --> pdb=" O ASP N 100Q" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.397A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 6.741A 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: 4.744A 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: 4.626A 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 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.713A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.628A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.709A 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=AE3, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.709A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.860A 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=AE4, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.517A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 11 through 12 removed outlier: 7.109A pdb=" N CYS P 92 " --> pdb=" O TRP P 101 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP P 101 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR P 94 " --> pdb=" O ASP P 100Q" (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.391A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 19 through 23 728 hydrogen bonds defined for protein. 1842 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: 3.81 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5038 1.32 - 1.47: 7214 1.47 - 1.61: 8835 1.61 - 1.75: 9 1.75 - 1.89: 138 Bond restraints: 21234 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.613 0.195 3.30e-02 9.18e+02 3.49e+01 bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.615 0.193 3.30e-02 9.18e+02 3.43e+01 bond pdb=" CA THR E 137 " pdb=" C THR E 137 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.33e-02 5.65e+03 2.76e+01 bond pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 1.502 1.384 0.118 2.30e-02 1.89e+03 2.62e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.61e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 24984 2.55 - 5.09: 3426 5.09 - 7.64: 379 7.64 - 10.19: 65 10.19 - 12.73: 12 Bond angle restraints: 28866 Sorted by residual: angle pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 113.80 122.57 -8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 113.80 122.51 -8.71 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 113.80 122.49 -8.69 1.00e+00 1.00e+00 7.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.09 -8.22 1.04e+00 9.25e-01 6.25e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.08 -8.21 1.04e+00 9.25e-01 6.23e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 14110 22.45 - 44.90: 360 44.90 - 67.34: 120 67.34 - 89.79: 104 89.79 - 112.24: 72 Dihedral angle restraints: 14766 sinusoidal: 7890 harmonic: 6876 Sorted by residual: dihedral pdb=" C PHE C 159 " pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " ideal model delta harmonic sigma weight residual -122.60 -107.87 -14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" C PHE A 159 " pdb=" N PHE A 159 " pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " ideal model delta harmonic sigma weight residual -122.60 -107.96 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C PHE E 159 " pdb=" N PHE E 159 " pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " ideal model delta harmonic sigma weight residual -122.60 -108.02 -14.58 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 14763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2533 0.108 - 0.216: 1010 0.216 - 0.324: 142 0.324 - 0.432: 32 0.432 - 0.540: 6 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.43e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.094 2.00e-02 2.50e+03 9.89e-02 1.22e+02 pdb=" CG ASN D 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.159 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.094 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" CG ASN F 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.094 2.00e-02 2.50e+03 9.85e-02 1.21e+02 pdb=" CG ASN B 611 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.116 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2997 2.73 - 3.28: 18807 3.28 - 3.82: 34213 3.82 - 4.36: 41635 4.36 - 4.90: 67793 Nonbonded interactions: 165445 Sorted by model distance: nonbonded pdb=" O4 MAN G 5 " pdb=" O6 MAN G 5 " model vdw 2.194 3.040 nonbonded pdb=" O4 MAN o 8 " pdb=" O6 MAN o 8 " model vdw 2.232 3.040 nonbonded pdb=" O5 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.255 2.432 nonbonded pdb=" O4 MAN o 5 " pdb=" O6 MAN o 5 " model vdw 2.257 3.040 nonbonded pdb=" O4 MAN a 5 " pdb=" O6 MAN a 5 " model vdw 2.270 3.040 ... (remaining 165440 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 'I' selection = chain 'J' selection = chain 'K' 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 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.700 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 0.195 21432 Z= 1.090 Angle : 1.856 13.558 29421 Z= 1.125 Chirality : 0.111 0.540 3723 Planarity : 0.009 0.051 3429 Dihedral : 15.746 112.236 10203 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.20 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 0.19 % Favored : 99.57 % Cbeta Deviations : 0.18 % 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: 0.80 (0.17), residues: 2325 helix: -0.63 (0.25), residues: 396 sheet: 0.83 (0.19), residues: 708 loop : 0.97 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 66 TYR 0.045 0.007 TYR N 100O PHE 0.057 0.009 PHE A 159 TRP 0.047 0.009 TRP A 96 HIS 0.008 0.002 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.01995 (21234) covalent geometry : angle 1.79975 (28866) SS BOND : bond 0.04797 ( 39) SS BOND : angle 3.37946 ( 78) hydrogen bonds : bond 0.16285 ( 689) hydrogen bonds : angle 7.62873 ( 1842) link_ALPHA1-2 : bond 0.06652 ( 12) link_ALPHA1-2 : angle 4.75431 ( 36) link_ALPHA1-3 : bond 0.06026 ( 15) link_ALPHA1-3 : angle 5.61496 ( 45) link_ALPHA1-6 : bond 0.05868 ( 21) link_ALPHA1-6 : angle 3.33774 ( 63) link_BETA1-4 : bond 0.06091 ( 60) link_BETA1-4 : angle 4.02336 ( 180) link_NAG-ASN : bond 0.07544 ( 51) link_NAG-ASN : angle 2.68420 ( 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 523 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 518 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7848 (mmm160) REVERT: A 99 ASN cc_start: 0.8375 (t0) cc_final: 0.8026 (t0) REVERT: A 325 ASP cc_start: 0.8135 (m-30) cc_final: 0.7866 (m-30) REVERT: H 13 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7800 (mmmt) REVERT: H 100 LYS cc_start: 0.7839 (mttt) cc_final: 0.7500 (mtpp) REVERT: L 58 ILE cc_start: 0.8515 (mm) cc_final: 0.8258 (mm) REVERT: C 46 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7412 (mtmm) REVERT: C 66 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7766 (tpt170) REVERT: C 103 GLN cc_start: 0.8005 (tt0) cc_final: 0.7795 (tt0) REVERT: D 608 VAL cc_start: 0.7631 (t) cc_final: 0.7409 (m) REVERT: D 625 ASN cc_start: 0.7414 (m-40) cc_final: 0.7048 (t0) REVERT: N 13 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7882 (mmmt) REVERT: N 100 LYS cc_start: 0.7946 (mttt) cc_final: 0.7630 (mtpp) REVERT: E 46 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7273 (mtmm) REVERT: E 66 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7919 (mmm160) REVERT: E 99 ASN cc_start: 0.8205 (t0) cc_final: 0.7875 (t0) REVERT: E 348 LYS cc_start: 0.7335 (tptt) cc_final: 0.6509 (mptt) REVERT: E 498 PRO cc_start: 0.6550 (Cg_endo) cc_final: 0.6243 (Cg_exo) REVERT: P 13 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7929 (mmmt) REVERT: P 100 LYS cc_start: 0.7886 (mttt) cc_final: 0.7528 (mtpp) outliers start: 5 outliers final: 5 residues processed: 523 average time/residue: 0.1786 time to fit residues: 135.0423 Evaluate side-chains 284 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 279 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 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: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 650 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN F 650 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139637 restraints weight = 29855.884| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.96 r_work: 0.3389 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21432 Z= 0.183 Angle : 0.859 10.894 29421 Z= 0.404 Chirality : 0.052 0.365 3723 Planarity : 0.005 0.054 3429 Dihedral : 13.235 86.238 5755 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 2.56 % Allowed : 7.45 % Favored : 89.98 % 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: 0.55 (0.17), residues: 2325 helix: 0.63 (0.28), residues: 351 sheet: 0.53 (0.19), residues: 669 loop : 0.34 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 350 TYR 0.018 0.002 TYR N 91 PHE 0.019 0.003 PHE C 391 TRP 0.025 0.002 TRP A 479 HIS 0.007 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00402 (21234) covalent geometry : angle 0.77006 (28866) SS BOND : bond 0.00460 ( 39) SS BOND : angle 1.23226 ( 78) hydrogen bonds : bond 0.05100 ( 689) hydrogen bonds : angle 6.28332 ( 1842) link_ALPHA1-2 : bond 0.01502 ( 12) link_ALPHA1-2 : angle 3.22755 ( 36) link_ALPHA1-3 : bond 0.01710 ( 15) link_ALPHA1-3 : angle 3.36112 ( 45) link_ALPHA1-6 : bond 0.00713 ( 21) link_ALPHA1-6 : angle 1.76238 ( 63) link_BETA1-4 : bond 0.00801 ( 60) link_BETA1-4 : angle 3.24918 ( 180) link_NAG-ASN : bond 0.00545 ( 51) link_NAG-ASN : angle 3.14115 ( 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 406 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 352 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LYS cc_start: 0.7678 (tptt) cc_final: 0.6845 (mptt) REVERT: H 13 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7824 (mmmt) REVERT: H 77 LEU cc_start: 0.7954 (mm) cc_final: 0.7558 (mm) REVERT: H 100 LYS cc_start: 0.7852 (mttt) cc_final: 0.7556 (mtpp) REVERT: L 25 GLU cc_start: 0.7875 (pp20) cc_final: 0.7516 (pp20) REVERT: C 350 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.6003 (ttm-80) REVERT: N 13 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7914 (mmmt) REVERT: N 77 LEU cc_start: 0.7688 (mm) cc_final: 0.7380 (mm) REVERT: N 100 LYS cc_start: 0.7969 (mttt) cc_final: 0.7717 (mtpp) REVERT: E 66 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7889 (mmm160) REVERT: E 99 ASN cc_start: 0.8197 (t0) cc_final: 0.7922 (t0) REVERT: E 195 ASN cc_start: 0.7379 (p0) cc_final: 0.7115 (p0) REVERT: F 653 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8083 (mm-40) REVERT: P 13 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7812 (mmmt) REVERT: P 29 VAL cc_start: 0.8122 (p) cc_final: 0.7818 (t) REVERT: P 66 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6987 (ptm-80) REVERT: P 77 LEU cc_start: 0.7870 (mm) cc_final: 0.7625 (mm) REVERT: P 81 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.6935 (mtt90) REVERT: P 100 LYS cc_start: 0.7888 (mttt) cc_final: 0.7557 (mtpp) REVERT: O 25 GLU cc_start: 0.7692 (pp20) cc_final: 0.7194 (pp20) REVERT: O 51 ASN cc_start: 0.7761 (m-40) cc_final: 0.7527 (m-40) outliers start: 54 outliers final: 28 residues processed: 389 average time/residue: 0.1615 time to fit residues: 94.2626 Evaluate side-chains 304 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 0.4980 chunk 128 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN C 103 GLN C 114 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141374 restraints weight = 29925.717| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.89 r_work: 0.3375 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21432 Z= 0.148 Angle : 0.765 10.441 29421 Z= 0.356 Chirality : 0.050 0.382 3723 Planarity : 0.004 0.066 3429 Dihedral : 11.149 83.602 5745 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.28 % Allowed : 9.59 % Favored : 88.13 % 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: 0.43 (0.17), residues: 2325 helix: 0.85 (0.28), residues: 351 sheet: 0.42 (0.18), residues: 663 loop : 0.17 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 503 TYR 0.014 0.001 TYR A 486 PHE 0.016 0.002 PHE E 159 TRP 0.024 0.002 TRP B 628 HIS 0.005 0.001 HIS H 3 Details of bonding type rmsd covalent geometry : bond 0.00319 (21234) covalent geometry : angle 0.68327 (28866) SS BOND : bond 0.00419 ( 39) SS BOND : angle 1.01656 ( 78) hydrogen bonds : bond 0.03991 ( 689) hydrogen bonds : angle 5.84551 ( 1842) link_ALPHA1-2 : bond 0.01366 ( 12) link_ALPHA1-2 : angle 3.46440 ( 36) link_ALPHA1-3 : bond 0.01499 ( 15) link_ALPHA1-3 : angle 3.39157 ( 45) link_ALPHA1-6 : bond 0.00637 ( 21) link_ALPHA1-6 : angle 1.61974 ( 63) link_BETA1-4 : bond 0.00811 ( 60) link_BETA1-4 : angle 2.83350 ( 180) link_NAG-ASN : bond 0.00465 ( 51) link_NAG-ASN : angle 2.66811 ( 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 356 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 308 time to evaluate : 0.787 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: A 66 ARG cc_start: 0.7638 (mmm160) cc_final: 0.6988 (tpm170) REVERT: A 225 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 348 LYS cc_start: 0.7779 (tptt) cc_final: 0.6900 (mptt) REVERT: B 592 LEU cc_start: 0.8715 (tp) cc_final: 0.8404 (mp) REVERT: B 647 GLU cc_start: 0.5308 (tt0) cc_final: 0.5002 (tt0) REVERT: H 13 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7848 (mmmt) REVERT: H 30 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7807 (tpp80) REVERT: H 77 LEU cc_start: 0.8060 (mm) cc_final: 0.7578 (mm) REVERT: H 100 LYS cc_start: 0.7934 (mttt) cc_final: 0.7623 (mtpp) REVERT: L 25 GLU cc_start: 0.7720 (pp20) cc_final: 0.7494 (pp20) REVERT: C 66 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7621 (tpm170) REVERT: C 67 ASN cc_start: 0.7403 (t0) cc_final: 0.7182 (t0) REVERT: N 13 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7922 (mmmt) REVERT: N 30 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8062 (tpp80) REVERT: N 77 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (mm) REVERT: N 100 LYS cc_start: 0.8035 (mttt) cc_final: 0.7764 (mtpp) REVERT: E 99 ASN cc_start: 0.8227 (t0) cc_final: 0.7949 (t0) REVERT: F 542 ARG cc_start: 0.7882 (tpt-90) cc_final: 0.7605 (ttt-90) REVERT: F 592 LEU cc_start: 0.8660 (tp) cc_final: 0.8321 (mp) REVERT: P 13 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7851 (mmmt) REVERT: P 29 VAL cc_start: 0.8160 (p) cc_final: 0.7956 (t) REVERT: P 66 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6974 (ptm-80) REVERT: P 77 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7579 (mm) REVERT: P 81 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7001 (mtt90) REVERT: P 100 LYS cc_start: 0.7966 (mttt) cc_final: 0.7640 (mtpp) outliers start: 48 outliers final: 25 residues processed: 335 average time/residue: 0.1522 time to fit residues: 77.6965 Evaluate side-chains 292 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 50 optimal weight: 0.4980 chunk 218 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 432 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 575 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134658 restraints weight = 30075.288| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.91 r_work: 0.3295 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21432 Z= 0.231 Angle : 0.804 12.007 29421 Z= 0.375 Chirality : 0.053 0.589 3723 Planarity : 0.005 0.074 3429 Dihedral : 10.507 89.781 5745 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.71 % Allowed : 10.07 % Favored : 87.23 % 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: -0.02 (0.16), residues: 2325 helix: 0.32 (0.27), residues: 369 sheet: 0.24 (0.18), residues: 642 loop : -0.15 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 20 TYR 0.015 0.002 TYR L 49 PHE 0.026 0.003 PHE H 100K TRP 0.043 0.002 TRP D 610 HIS 0.007 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00548 (21234) covalent geometry : angle 0.72299 (28866) SS BOND : bond 0.00731 ( 39) SS BOND : angle 1.33394 ( 78) hydrogen bonds : bond 0.04183 ( 689) hydrogen bonds : angle 5.87181 ( 1842) link_ALPHA1-2 : bond 0.01111 ( 12) link_ALPHA1-2 : angle 3.33228 ( 36) link_ALPHA1-3 : bond 0.01278 ( 15) link_ALPHA1-3 : angle 3.09868 ( 45) link_ALPHA1-6 : bond 0.00490 ( 21) link_ALPHA1-6 : angle 1.81225 ( 63) link_BETA1-4 : bond 0.00707 ( 60) link_BETA1-4 : angle 2.95709 ( 180) link_NAG-ASN : bond 0.00609 ( 51) link_NAG-ASN : angle 2.79497 ( 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 340 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8052 (ptpp) REVERT: A 66 ARG cc_start: 0.7585 (mmm160) cc_final: 0.6943 (tpm170) REVERT: A 225 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7903 (mt) REVERT: A 348 LYS cc_start: 0.7696 (tptt) cc_final: 0.6977 (mptt) REVERT: B 626 MET cc_start: 0.6781 (mtt) cc_final: 0.6451 (mtp) REVERT: H 30 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7778 (tpp80) REVERT: H 66 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (ptm160) REVERT: H 73 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7811 (ttmm) REVERT: H 77 LEU cc_start: 0.7931 (mm) cc_final: 0.7517 (mm) REVERT: H 100 LYS cc_start: 0.8072 (mttt) cc_final: 0.7713 (mtpp) REVERT: L 25 GLU cc_start: 0.7789 (pp20) cc_final: 0.7496 (pp20) REVERT: C 69 TRP cc_start: 0.8728 (m-90) cc_final: 0.8499 (m-90) REVERT: D 542 ARG cc_start: 0.8052 (tpt-90) cc_final: 0.7813 (ttt-90) REVERT: N 13 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8074 (mmmt) REVERT: N 77 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7486 (mm) REVERT: N 100 LYS cc_start: 0.8175 (mttt) cc_final: 0.7882 (mtpp) REVERT: M 25 GLU cc_start: 0.7613 (pp20) cc_final: 0.7389 (pp20) REVERT: P 13 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7875 (mmmt) REVERT: P 66 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7092 (mtp180) REVERT: P 77 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7518 (mm) REVERT: P 81 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.7057 (mtt90) REVERT: P 100 LYS cc_start: 0.8143 (mttt) cc_final: 0.7825 (mtpp) outliers start: 57 outliers final: 31 residues processed: 322 average time/residue: 0.1522 time to fit residues: 74.1961 Evaluate side-chains 293 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 73 LYS Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 195 optimal weight: 0.0040 chunk 72 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 302 ASN B 591 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 300 ASN C 302 ASN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137793 restraints weight = 29596.272| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.53 r_work: 0.3374 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21432 Z= 0.126 Angle : 0.711 11.125 29421 Z= 0.331 Chirality : 0.049 0.485 3723 Planarity : 0.004 0.082 3429 Dihedral : 9.600 82.760 5745 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 11.11 % Favored : 86.66 % 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: 0.09 (0.17), residues: 2325 helix: 0.65 (0.28), residues: 369 sheet: 0.31 (0.20), residues: 606 loop : -0.14 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 20 TYR 0.016 0.001 TYR A 486 PHE 0.016 0.002 PHE P 100K TRP 0.022 0.001 TRP F 631 HIS 0.004 0.001 HIS H 3 Details of bonding type rmsd covalent geometry : bond 0.00263 (21234) covalent geometry : angle 0.62922 (28866) SS BOND : bond 0.00414 ( 39) SS BOND : angle 1.60970 ( 78) hydrogen bonds : bond 0.03429 ( 689) hydrogen bonds : angle 5.47653 ( 1842) link_ALPHA1-2 : bond 0.01107 ( 12) link_ALPHA1-2 : angle 3.05588 ( 36) link_ALPHA1-3 : bond 0.01431 ( 15) link_ALPHA1-3 : angle 3.09693 ( 45) link_ALPHA1-6 : bond 0.00628 ( 21) link_ALPHA1-6 : angle 1.63775 ( 63) link_BETA1-4 : bond 0.00704 ( 60) link_BETA1-4 : angle 2.69189 ( 180) link_NAG-ASN : bond 0.00389 ( 51) link_NAG-ASN : angle 2.57323 ( 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 341 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7042 (tpm170) REVERT: A 225 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 392 ASN cc_start: 0.4694 (t0) cc_final: 0.4307 (t0) REVERT: H 30 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7784 (tpp80) REVERT: H 77 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7715 (mm) REVERT: H 100 LYS cc_start: 0.8149 (mttt) cc_final: 0.7873 (mtpp) REVERT: L 25 GLU cc_start: 0.7729 (pp20) cc_final: 0.7417 (pp20) REVERT: C 69 TRP cc_start: 0.8681 (m-90) cc_final: 0.8421 (m-90) REVERT: N 13 LYS cc_start: 0.8215 (mmtt) cc_final: 0.8002 (mmmt) REVERT: N 30 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8026 (tpp80) REVERT: N 77 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7583 (mm) REVERT: N 100 LYS cc_start: 0.8194 (mttt) cc_final: 0.7917 (mtpp) REVERT: M 25 GLU cc_start: 0.7536 (pp20) cc_final: 0.7262 (pp20) REVERT: E 217 TYR cc_start: 0.8478 (m-10) cc_final: 0.8209 (m-10) REVERT: F 530 MET cc_start: 0.5602 (mtt) cc_final: 0.5048 (mtt) REVERT: P 13 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7806 (mmmt) REVERT: P 66 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7000 (ptm-80) REVERT: P 77 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (mm) REVERT: P 81 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7034 (mtt90) REVERT: P 100 LYS cc_start: 0.8247 (mttt) cc_final: 0.7878 (mtpp) outliers start: 47 outliers final: 23 residues processed: 317 average time/residue: 0.1508 time to fit residues: 73.2209 Evaluate side-chains 295 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 50 ASN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132594 restraints weight = 29919.895| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.96 r_work: 0.3267 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21432 Z= 0.256 Angle : 0.812 10.852 29421 Z= 0.381 Chirality : 0.053 0.464 3723 Planarity : 0.005 0.081 3429 Dihedral : 9.967 93.365 5745 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.56 % Allowed : 11.63 % Favored : 85.80 % 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: -0.13 (0.16), residues: 2325 helix: 0.50 (0.28), residues: 369 sheet: 0.19 (0.20), residues: 564 loop : -0.30 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 20 TYR 0.019 0.002 TYR M 49 PHE 0.026 0.003 PHE H 100K TRP 0.030 0.002 TRP F 610 HIS 0.008 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00614 (21234) covalent geometry : angle 0.73301 (28866) SS BOND : bond 0.00465 ( 39) SS BOND : angle 1.83274 ( 78) hydrogen bonds : bond 0.04110 ( 689) hydrogen bonds : angle 5.83719 ( 1842) link_ALPHA1-2 : bond 0.00969 ( 12) link_ALPHA1-2 : angle 3.16280 ( 36) link_ALPHA1-3 : bond 0.01248 ( 15) link_ALPHA1-3 : angle 3.01548 ( 45) link_ALPHA1-6 : bond 0.00498 ( 21) link_ALPHA1-6 : angle 1.77309 ( 63) link_BETA1-4 : bond 0.00678 ( 60) link_BETA1-4 : angle 2.87359 ( 180) link_NAG-ASN : bond 0.00540 ( 51) link_NAG-ASN : angle 2.79232 ( 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 334 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7668 (mmm160) cc_final: 0.7053 (tpm170) REVERT: A 225 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7933 (mt) REVERT: A 348 LYS cc_start: 0.7707 (tptt) cc_final: 0.6893 (mptt) REVERT: A 392 ASN cc_start: 0.5075 (t0) cc_final: 0.4871 (t0) REVERT: A 475 MET cc_start: 0.8781 (mmm) cc_final: 0.8363 (mmp) REVERT: B 530 MET cc_start: 0.5968 (mtt) cc_final: 0.5634 (mtt) REVERT: H 30 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7815 (tpp80) REVERT: H 77 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7910 (mm) REVERT: H 100 LYS cc_start: 0.8146 (mttt) cc_final: 0.7880 (mtpp) REVERT: L 25 GLU cc_start: 0.7677 (pp20) cc_final: 0.7325 (pp20) REVERT: C 92 ASN cc_start: 0.7668 (m-40) cc_final: 0.7411 (t0) REVERT: D 523 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 591 GLN cc_start: 0.7898 (tt0) cc_final: 0.7689 (tt0) REVERT: N 13 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8082 (mmmt) REVERT: N 30 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8102 (tpp80) REVERT: N 77 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7668 (mm) REVERT: N 100 LYS cc_start: 0.8231 (mttt) cc_final: 0.7983 (mtpp) REVERT: M 25 GLU cc_start: 0.7667 (pp20) cc_final: 0.7322 (pp20) REVERT: E 159 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: E 411 ASN cc_start: 0.7024 (p0) cc_final: 0.6688 (p0) REVERT: F 530 MET cc_start: 0.6055 (mtt) cc_final: 0.5617 (mtt) REVERT: F 608 VAL cc_start: 0.8414 (m) cc_final: 0.8135 (p) REVERT: F 610 TRP cc_start: 0.6726 (m100) cc_final: 0.6505 (m100) REVERT: P 13 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7763 (mmmt) REVERT: P 66 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6815 (mtp180) REVERT: P 77 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7522 (mm) REVERT: P 100 LYS cc_start: 0.8295 (mttt) cc_final: 0.7988 (mtpp) outliers start: 54 outliers final: 39 residues processed: 318 average time/residue: 0.1515 time to fit residues: 73.4461 Evaluate side-chains 305 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136953 restraints weight = 30107.301| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.80 r_work: 0.3302 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21432 Z= 0.175 Angle : 0.747 11.887 29421 Z= 0.349 Chirality : 0.050 0.363 3723 Planarity : 0.005 0.083 3429 Dihedral : 9.706 91.130 5745 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.37 % Allowed : 12.87 % Favored : 84.76 % 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: -0.09 (0.16), residues: 2325 helix: 0.59 (0.28), residues: 369 sheet: 0.52 (0.21), residues: 522 loop : -0.42 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 20 TYR 0.011 0.002 TYR H 100O PHE 0.018 0.002 PHE H 100K TRP 0.018 0.002 TRP D 610 HIS 0.006 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00408 (21234) covalent geometry : angle 0.66558 (28866) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.59001 ( 78) hydrogen bonds : bond 0.03675 ( 689) hydrogen bonds : angle 5.64550 ( 1842) link_ALPHA1-2 : bond 0.00970 ( 12) link_ALPHA1-2 : angle 2.99067 ( 36) link_ALPHA1-3 : bond 0.01333 ( 15) link_ALPHA1-3 : angle 2.99551 ( 45) link_ALPHA1-6 : bond 0.00542 ( 21) link_ALPHA1-6 : angle 1.66766 ( 63) link_BETA1-4 : bond 0.00647 ( 60) link_BETA1-4 : angle 2.73541 ( 180) link_NAG-ASN : bond 0.00408 ( 51) link_NAG-ASN : angle 2.78988 ( 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 321 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.809 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: A 225 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7942 (mt) REVERT: H 30 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7773 (tpp80) REVERT: H 100 LYS cc_start: 0.8300 (mttt) cc_final: 0.7985 (mtpp) REVERT: L 25 GLU cc_start: 0.7494 (pp20) cc_final: 0.7137 (pp20) REVERT: C 66 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7610 (mtm110) REVERT: C 69 TRP cc_start: 0.8677 (m-90) cc_final: 0.8358 (m-90) REVERT: N 13 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7974 (mmmt) REVERT: N 30 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8132 (tpp80) REVERT: N 77 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7649 (mm) REVERT: N 100 LYS cc_start: 0.8200 (mttt) cc_final: 0.7964 (mtpp) REVERT: M 25 GLU cc_start: 0.7533 (pp20) cc_final: 0.7184 (pp20) REVERT: F 530 MET cc_start: 0.6025 (mtt) cc_final: 0.5579 (mtt) REVERT: F 608 VAL cc_start: 0.8357 (m) cc_final: 0.8141 (p) REVERT: F 626 MET cc_start: 0.6499 (mtp) cc_final: 0.6214 (ttm) REVERT: P 13 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7880 (mmmt) REVERT: P 77 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7481 (mm) REVERT: P 100 LYS cc_start: 0.8276 (mttt) cc_final: 0.7946 (mtpp) outliers start: 50 outliers final: 35 residues processed: 304 average time/residue: 0.1573 time to fit residues: 72.8494 Evaluate side-chains 291 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN ** P 68 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 = 0.3912 r_free = 0.3912 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133599 restraints weight = 29844.369| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.73 r_work: 0.3257 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21432 Z= 0.265 Angle : 0.834 14.913 29421 Z= 0.390 Chirality : 0.053 0.386 3723 Planarity : 0.005 0.085 3429 Dihedral : 10.136 97.973 5745 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.75 % Allowed : 12.68 % Favored : 84.57 % 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: -0.40 (0.17), residues: 2325 helix: 0.38 (0.27), residues: 369 sheet: 0.10 (0.20), residues: 585 loop : -0.57 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 20 TYR 0.016 0.002 TYR L 49 PHE 0.024 0.003 PHE H 100K TRP 0.023 0.002 TRP F 571 HIS 0.016 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00640 (21234) covalent geometry : angle 0.75088 (28866) SS BOND : bond 0.00518 ( 39) SS BOND : angle 1.88002 ( 78) hydrogen bonds : bond 0.04190 ( 689) hydrogen bonds : angle 5.93499 ( 1842) link_ALPHA1-2 : bond 0.00862 ( 12) link_ALPHA1-2 : angle 3.06263 ( 36) link_ALPHA1-3 : bond 0.01178 ( 15) link_ALPHA1-3 : angle 2.95196 ( 45) link_ALPHA1-6 : bond 0.00504 ( 21) link_ALPHA1-6 : angle 1.76515 ( 63) link_BETA1-4 : bond 0.00649 ( 60) link_BETA1-4 : angle 2.85783 ( 180) link_NAG-ASN : bond 0.00613 ( 51) link_NAG-ASN : angle 3.17176 ( 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 327 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.787 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: A 225 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7932 (mt) REVERT: A 350 ARG cc_start: 0.6436 (ttm-80) cc_final: 0.6106 (tpp80) REVERT: H 30 ARG cc_start: 0.8448 (ttp80) cc_final: 0.7788 (tpp80) REVERT: H 100 LYS cc_start: 0.8259 (mttt) cc_final: 0.7980 (mtpp) REVERT: C 66 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7794 (mtm110) REVERT: D 612 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8558 (p) REVERT: N 13 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8055 (mmmt) REVERT: N 30 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8160 (tpp80) REVERT: N 77 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7688 (mm) REVERT: N 81 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7214 (mtm110) REVERT: N 100 LYS cc_start: 0.8223 (mttt) cc_final: 0.7947 (mtpp) REVERT: E 159 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: E 411 ASN cc_start: 0.7064 (p0) cc_final: 0.6769 (p0) REVERT: F 530 MET cc_start: 0.5835 (mtt) cc_final: 0.5582 (mtt) REVERT: P 13 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7897 (mmmt) REVERT: P 77 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7533 (mm) REVERT: P 100 LYS cc_start: 0.8323 (mttt) cc_final: 0.7987 (mtpp) outliers start: 58 outliers final: 44 residues processed: 309 average time/residue: 0.1535 time to fit residues: 72.3210 Evaluate side-chains 305 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 0.7980 chunk 213 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 150 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.163620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139027 restraints weight = 29928.204| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.69 r_work: 0.3335 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21432 Z= 0.137 Angle : 0.722 12.202 29421 Z= 0.338 Chirality : 0.048 0.318 3723 Planarity : 0.004 0.088 3429 Dihedral : 9.433 89.699 5745 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 13.58 % Favored : 84.33 % 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: -0.23 (0.17), residues: 2325 helix: 0.60 (0.28), residues: 369 sheet: 0.29 (0.21), residues: 552 loop : -0.50 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 20 TYR 0.011 0.001 TYR H 100O PHE 0.017 0.002 PHE P 100K TRP 0.017 0.001 TRP D 610 HIS 0.006 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00304 (21234) covalent geometry : angle 0.64239 (28866) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.48369 ( 78) hydrogen bonds : bond 0.03387 ( 689) hydrogen bonds : angle 5.51559 ( 1842) link_ALPHA1-2 : bond 0.00882 ( 12) link_ALPHA1-2 : angle 2.76068 ( 36) link_ALPHA1-3 : bond 0.01400 ( 15) link_ALPHA1-3 : angle 2.92618 ( 45) link_ALPHA1-6 : bond 0.00614 ( 21) link_ALPHA1-6 : angle 1.61912 ( 63) link_BETA1-4 : bond 0.00642 ( 60) link_BETA1-4 : angle 2.62673 ( 180) link_NAG-ASN : bond 0.00321 ( 51) link_NAG-ASN : angle 2.76018 ( 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 319 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.773 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: A 225 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7866 (mt) REVERT: A 350 ARG cc_start: 0.6404 (ttm-80) cc_final: 0.6063 (tpp80) REVERT: H 30 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7837 (tpp80) REVERT: H 100 LYS cc_start: 0.8262 (mttt) cc_final: 0.7973 (mtpp) REVERT: L 25 GLU cc_start: 0.7458 (pp20) cc_final: 0.7230 (pp20) REVERT: C 66 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7749 (mtm110) REVERT: C 69 TRP cc_start: 0.8686 (m-90) cc_final: 0.8280 (m-90) REVERT: D 612 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8477 (p) REVERT: N 13 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7913 (mmmt) REVERT: N 30 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8126 (tpp80) REVERT: N 77 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7686 (mm) REVERT: N 81 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7270 (mtm110) REVERT: N 100 LYS cc_start: 0.8172 (mttt) cc_final: 0.7882 (mtpp) REVERT: E 66 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8056 (mtm-85) REVERT: F 530 MET cc_start: 0.5696 (mtt) cc_final: 0.5414 (mtt) REVERT: F 626 MET cc_start: 0.6655 (mtp) cc_final: 0.6451 (ttm) REVERT: P 13 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7834 (mmmt) REVERT: P 77 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7509 (mm) REVERT: P 100 LYS cc_start: 0.8316 (mttt) cc_final: 0.7963 (mtpp) outliers start: 44 outliers final: 32 residues processed: 304 average time/residue: 0.1522 time to fit residues: 70.5887 Evaluate side-chains 295 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 141 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 177 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133348 restraints weight = 30183.875| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.96 r_work: 0.3285 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21432 Z= 0.174 Angle : 0.748 11.664 29421 Z= 0.349 Chirality : 0.049 0.327 3723 Planarity : 0.005 0.089 3429 Dihedral : 9.407 90.897 5745 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.99 % Allowed : 13.49 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2325 helix: 0.60 (0.28), residues: 369 sheet: 0.28 (0.21), residues: 561 loop : -0.50 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 20 TYR 0.011 0.002 TYR M 49 PHE 0.018 0.002 PHE H 100K TRP 0.019 0.002 TRP F 610 HIS 0.009 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00406 (21234) covalent geometry : angle 0.67054 (28866) SS BOND : bond 0.00450 ( 39) SS BOND : angle 1.76918 ( 78) hydrogen bonds : bond 0.03589 ( 689) hydrogen bonds : angle 5.54232 ( 1842) link_ALPHA1-2 : bond 0.00823 ( 12) link_ALPHA1-2 : angle 2.75031 ( 36) link_ALPHA1-3 : bond 0.01305 ( 15) link_ALPHA1-3 : angle 2.92728 ( 45) link_ALPHA1-6 : bond 0.00541 ( 21) link_ALPHA1-6 : angle 1.67934 ( 63) link_BETA1-4 : bond 0.00634 ( 60) link_BETA1-4 : angle 2.63826 ( 180) link_NAG-ASN : bond 0.00381 ( 51) link_NAG-ASN : angle 2.72662 ( 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 298 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.733 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: A 225 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 392 ASN cc_start: 0.4915 (t0) cc_final: 0.4553 (t0) REVERT: H 100 LYS cc_start: 0.8250 (mttt) cc_final: 0.7963 (mtpp) REVERT: C 66 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7585 (ttp80) REVERT: C 69 TRP cc_start: 0.8684 (m-90) cc_final: 0.8323 (m-90) REVERT: C 426 MET cc_start: 0.8268 (mtp) cc_final: 0.7985 (mtp) REVERT: D 612 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8605 (p) REVERT: N 13 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8031 (mmmt) REVERT: N 30 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8125 (tpp80) REVERT: N 77 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7789 (mm) REVERT: N 81 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7279 (mtm110) REVERT: N 100 LYS cc_start: 0.8317 (mttt) cc_final: 0.7989 (mtpp) REVERT: E 66 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8008 (mtm-85) REVERT: E 159 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: E 411 ASN cc_start: 0.7132 (p0) cc_final: 0.6807 (p0) REVERT: P 13 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7894 (mmmt) REVERT: P 77 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7568 (mm) REVERT: P 100 LYS cc_start: 0.8348 (mttt) cc_final: 0.7987 (mtpp) outliers start: 42 outliers final: 32 residues processed: 282 average time/residue: 0.1536 time to fit residues: 66.3103 Evaluate side-chains 292 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134539 restraints weight = 30066.963| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.13 r_work: 0.3313 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21432 Z= 0.136 Angle : 0.710 10.520 29421 Z= 0.332 Chirality : 0.048 0.309 3723 Planarity : 0.004 0.087 3429 Dihedral : 9.050 85.887 5745 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 13.53 % Favored : 84.57 % 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: -0.18 (0.17), residues: 2325 helix: 0.62 (0.28), residues: 369 sheet: 0.31 (0.21), residues: 567 loop : -0.47 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.011 0.001 TYR C 486 PHE 0.017 0.002 PHE P 100K TRP 0.017 0.001 TRP D 610 HIS 0.006 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00306 (21234) covalent geometry : angle 0.63617 (28866) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.70327 ( 78) hydrogen bonds : bond 0.03281 ( 689) hydrogen bonds : angle 5.37646 ( 1842) link_ALPHA1-2 : bond 0.00813 ( 12) link_ALPHA1-2 : angle 2.60371 ( 36) link_ALPHA1-3 : bond 0.01390 ( 15) link_ALPHA1-3 : angle 2.90013 ( 45) link_ALPHA1-6 : bond 0.00604 ( 21) link_ALPHA1-6 : angle 1.61327 ( 63) link_BETA1-4 : bond 0.00639 ( 60) link_BETA1-4 : angle 2.53060 ( 180) link_NAG-ASN : bond 0.00314 ( 51) link_NAG-ASN : angle 2.55289 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.32 seconds wall clock time: 75 minutes 11.82 seconds (4511.82 seconds total)