Starting phenix.real_space_refine on Sun Jul 5 07:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.map" model { file = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lg6_23312/07_2026/7lg6_23312.cif" } resolution = 3.28 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= 0.010 sd= 0.097 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 147 5.16 5 C 16638 2.51 5 N 4443 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26550 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "E" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "O" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "Q" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "P" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "R" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" 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 chiralities: 8 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "l" 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 chiralities: 8 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "z" 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 chiralities: 8 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 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 chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Time building chain proxies: 7.18, per 1000 atoms: 0.27 Number of scatterers: 26550 At special positions: 0 Unit cell: (159.65, 150.38, 157.59, 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 147 16.00 O 5322 8.00 N 4443 7.00 C 16638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS G 561 " distance=2.01 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS I 561 " distance=2.01 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN k 4 " - " MAN k 5 " " MAN l 4 " - " MAN l 5 " " MAN y 4 " - " MAN y 5 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA k 3 " - " MAN k 6 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA y 3 " - " MAN y 6 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 7 1 " - " FUC 7 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG f 1 " - " FUC f 2 " " NAG t 1 " - " FUC t 2 " NAG-ASN " NAG 0 1 " - " ASN F 295 " " NAG 1 1 " - " ASN F 332 " " NAG 2 1 " - " ASN F 386 " " NAG 3 1 " - " ASN F 392 " " NAG 4 1 " - " ASN F 448 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 363 " " NAG 7 1 " - " ASN I 611 " " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 137 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 197 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 137 " " NAG F 601 " - " ASN F 197 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 137 " " NAG G 701 " - " ASN G 618 " " NAG G 702 " - " ASN G 637 " " NAG I 701 " - " ASN I 618 " " NAG I 702 " - " ASN I 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 160 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 295 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 448 " " NAG d 1 " - " ASN A 301 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN B 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 156 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 276 " " NAG m 1 " - " ASN E 295 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 386 " " NAG p 1 " - " ASN E 392 " " NAG q 1 " - " ASN E 448 " " NAG r 1 " - " ASN E 301 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN G 611 " " NAG u 1 " - " ASN F 88 " " NAG v 1 " - " ASN F 156 " " NAG w 1 " - " ASN F 160 " " NAG x 1 " - " ASN F 234 " " NAG y 1 " - " ASN F 262 " " NAG z 1 " - " ASN F 276 " Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.0 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 57 sheets defined 18.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.026A 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 139 through 151 Processing helix chain 'A' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.026A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.952A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 553 Processing helix chain 'G' and resid 561 through 568 removed outlier: 4.050A pdb=" N LEU G 565 " --> pdb=" O CYS G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 4.381A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 633 Processing helix chain 'G' and resid 635 through 637 No H-bonds generated for 'chain 'G' and resid 635 through 637' Processing helix chain 'G' and resid 638 through 658 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.027A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU F 342 " --> pdb=" O TRP F 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 553 Processing helix chain 'I' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU I 565 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 633 Processing helix chain 'I' and resid 635 through 637 No H-bonds generated for 'chain 'I' and resid 635 through 637' Processing helix chain 'I' and resid 638 through 658 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 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 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 82B" --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP C 35 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 50 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 5.470A pdb=" N ILE Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 82B" --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP J 35 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.020A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AE6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE7, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AE8, first strand: chain 'F' and resid 201 through 203 Processing sheet with id=AE9, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'P' and resid 56 through 59 removed outlier: 6.788A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE P 34 " --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'R' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR R 49 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 82B" --> pdb=" O GLU K 16 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP K 35 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 1047 hydrogen bonds defined for protein. 2691 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: 5.96 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5481 1.32 - 1.47: 9946 1.47 - 1.61: 11456 1.61 - 1.76: 54 1.76 - 1.91: 168 Bond restraints: 27105 Sorted by residual: bond pdb=" NE ARG D 3 " pdb=" CZ ARG D 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG M 3 " pdb=" CZ ARG M 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG N 3 " pdb=" CZ ARG N 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" CB ASP R 91 " pdb=" CG ASP R 91 " ideal model delta sigma weight residual 1.516 1.367 0.149 2.50e-02 1.60e+03 3.53e+01 bond pdb=" CB ASP Q 91 " pdb=" CG ASP Q 91 " ideal model delta sigma weight residual 1.516 1.368 0.148 2.50e-02 1.60e+03 3.52e+01 ... (remaining 27100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 33306 2.90 - 5.79: 3128 5.79 - 8.69: 358 8.69 - 11.58: 24 11.58 - 14.48: 6 Bond angle restraints: 36822 Sorted by residual: angle pdb=" C TRP P 72C" pdb=" N ARG P 72D" pdb=" CA ARG P 72D" ideal model delta sigma weight residual 120.28 134.76 -14.48 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP O 72C" pdb=" N ARG O 72D" pdb=" CA ARG O 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP H 72C" pdb=" N ARG H 72D" pdb=" CA ARG H 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" N SER G 613 " pdb=" CA SER G 613 " pdb=" C SER G 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 angle pdb=" N SER I 613 " pdb=" CA SER I 613 " pdb=" C SER I 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 14556 17.49 - 34.98: 408 34.98 - 52.47: 129 52.47 - 69.96: 54 69.96 - 87.45: 15 Dihedral angle restraints: 15162 sinusoidal: 6102 harmonic: 9060 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.62 -43.62 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 15159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2885 0.101 - 0.203: 1042 0.203 - 0.304: 340 0.304 - 0.406: 159 0.406 - 0.507: 77 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 ... (remaining 4500 not shown) Planarity restraints: 4563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.98e+01 pdb=" CG ASN E 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG E 603 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 133 " 0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN F 133 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN F 133 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN F 133 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 603 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN A 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.084 2.00e-02 2.50e+03 ... (remaining 4560 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 11239 2.92 - 3.41: 22833 3.41 - 3.91: 44050 3.91 - 4.40: 50557 4.40 - 4.90: 81424 Nonbonded interactions: 210103 Sorted by model distance: nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS F 46 " pdb=" OD2 ASP I 632 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP G 632 " model vdw 2.421 3.120 nonbonded pdb=" N GLY F 431 " pdb=" O GLY F 431 " model vdw 2.423 2.496 nonbonded pdb=" N GLY A 431 " pdb=" O GLY A 431 " model vdw 2.423 2.496 ... (remaining 210098 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: 0.07 Found NCS groups: ncs_group { reference = (chain '0' and resid 1) selection = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '3' and resid 1) selection = (chain '4' and resid 1) selection = (chain '5' and resid 1) selection = (chain '6' and resid 1) selection = (chain '7' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'u' and resid 1) selection = (chain 'w' and resid 1) selection = (chain 'x' and resid 1) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain 'X' selection = chain 'l' 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.450 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.023 0.149 27288 Z= 1.213 Angle : 1.832 14.479 37323 Z= 1.160 Chirality : 0.140 0.507 4503 Planarity : 0.009 0.038 4503 Dihedral : 10.306 87.455 9192 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.57 % Favored : 95.75 % Rotamer: Outliers : 0.33 % Allowed : 0.76 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.39 (0.15), residues: 3105 helix: -0.80 (0.23), residues: 477 sheet: 0.93 (0.16), residues: 1116 loop : 0.24 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 350 TYR 0.048 0.009 TYR F 177 PHE 0.034 0.006 PHE N 98 TRP 0.057 0.011 TRP F 479 HIS 0.015 0.003 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02283 / 1.19 (27105) covalent geometry : angle 1.79372 / 1.16 (36822) SS BOND : bond 0.00950 / 0.63 ( 48) SS BOND : angle 3.27140 / 2.36 ( 96) hydrogen bonds : bond 0.16743 / 11.45 ( 1002) hydrogen bonds : angle 7.75480 / 5.42 ( 2691) link_ALPHA1-2 : bond 0.08558 / 4.94 ( 6) link_ALPHA1-2 : angle 4.38696 / 2.75 ( 18) link_ALPHA1-3 : bond 0.07777 / 4.92 ( 9) link_ALPHA1-3 : angle 4.33422 / 2.97 ( 27) link_ALPHA1-6 : bond 0.05401 / 3.41 ( 9) link_ALPHA1-6 : angle 3.34445 / 2.31 ( 27) link_BETA1-4 : bond 0.07146 / 4.54 ( 48) link_BETA1-4 : angle 4.59270 / 3.34 ( 144) link_BETA1-6 : bond 0.08313 / 3.71 ( 3) link_BETA1-6 : angle 4.84408 / 3.00 ( 9) link_NAG-ASN : bond 0.07619 / 4.88 ( 60) link_NAG-ASN : angle 2.81522 / 1.95 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 637 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mtp85) REVERT: B 632 ASP cc_start: 0.8843 (t70) cc_final: 0.8600 (t0) REVERT: O 86 ASP cc_start: 0.8152 (m-30) cc_final: 0.7892 (m-30) REVERT: G 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8591 (t0) REVERT: P 86 ASP cc_start: 0.8259 (m-30) cc_final: 0.8005 (m-30) REVERT: I 632 ASP cc_start: 0.8851 (t70) cc_final: 0.8579 (t0) outliers start: 9 outliers final: 3 residues processed: 646 average time/residue: 0.2129 time to fit residues: 206.2084 Evaluate side-chains 355 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 351 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN H 10 GLN L 37 GLN D 92 ASN C 39 GLN E 195 ASN O 10 GLN Q 37 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN F 195 ASN N 92 ASN K 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079475 restraints weight = 50152.868| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.13 r_work: 0.3021 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27288 Z= 0.166 Angle : 0.777 10.293 37323 Z= 0.393 Chirality : 0.046 0.287 4503 Planarity : 0.004 0.042 4503 Dihedral : 5.508 41.419 3425 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.77 % Favored : 95.75 % Rotamer: Outliers : 1.78 % Allowed : 6.70 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.42 (0.15), residues: 3105 helix: 0.58 (0.27), residues: 459 sheet: 1.02 (0.15), residues: 1119 loop : -0.34 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 103 TYR 0.018 0.002 TYR F 61 PHE 0.015 0.002 PHE E 383 TRP 0.034 0.002 TRP D 96 HIS 0.006 0.002 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (27105) covalent geometry : angle 0.73285 / 0.38 (36822) SS BOND : bond 0.00386 / 0.24 ( 48) SS BOND : angle 1.35090 / 0.88 ( 96) hydrogen bonds : bond 0.05536 / 3.72 ( 1002) hydrogen bonds : angle 6.09281 / 4.26 ( 2691) link_ALPHA1-2 : bond 0.00577 / 0.32 ( 6) link_ALPHA1-2 : angle 2.04392 / 1.29 ( 18) link_ALPHA1-3 : bond 0.00921 / 0.58 ( 9) link_ALPHA1-3 : angle 1.38203 / 0.93 ( 27) link_ALPHA1-6 : bond 0.00646 / 0.40 ( 9) link_ALPHA1-6 : angle 1.64533 / 1.13 ( 27) link_BETA1-4 : bond 0.00624 / 0.40 ( 48) link_BETA1-4 : angle 2.41705 / 1.71 ( 144) link_BETA1-6 : bond 0.00977 / 0.44 ( 3) link_BETA1-6 : angle 0.84707 / 0.51 ( 9) link_NAG-ASN : bond 0.00532 / 0.35 ( 60) link_NAG-ASN : angle 2.91156 / 2.08 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 1.229 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: A 82 GLN cc_start: 0.8589 (mp10) cc_final: 0.8111 (mp10) REVERT: H 46 GLU cc_start: 0.7345 (tp30) cc_final: 0.6494 (tt0) REVERT: L 4 MET cc_start: 0.7437 (mmm) cc_final: 0.6210 (mmp) REVERT: L 17 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 632 ASP cc_start: 0.9122 (t70) cc_final: 0.8711 (t0) REVERT: B 652 GLN cc_start: 0.8322 (tp40) cc_final: 0.8111 (tp40) REVERT: D 81 GLU cc_start: 0.7935 (mp0) cc_final: 0.7552 (pm20) REVERT: D 90 GLN cc_start: 0.7623 (tp40) cc_final: 0.7232 (tp40) REVERT: C 48 ILE cc_start: 0.8986 (mt) cc_final: 0.8745 (tt) REVERT: C 72 ASP cc_start: 0.7254 (t0) cc_final: 0.6915 (p0) REVERT: C 77 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: E 65 LYS cc_start: 0.7402 (mttt) cc_final: 0.7176 (mtmm) REVERT: O 11 PHE cc_start: 0.7502 (m-80) cc_final: 0.7079 (m-80) REVERT: Q 4 MET cc_start: 0.6422 (mtt) cc_final: 0.5713 (mtt) REVERT: Q 86 TYR cc_start: 0.7748 (m-80) cc_final: 0.7503 (m-80) REVERT: Q 100 GLN cc_start: 0.7373 (mp10) cc_final: 0.7162 (mp10) REVERT: G 588 ARG cc_start: 0.8332 (tpt170) cc_final: 0.7587 (ttm110) REVERT: G 632 ASP cc_start: 0.9101 (t70) cc_final: 0.8688 (t0) REVERT: M 81 GLU cc_start: 0.8055 (mp0) cc_final: 0.7786 (pm20) REVERT: J 13 ARG cc_start: 0.6016 (mmt90) cc_final: 0.5459 (mpp-170) REVERT: P 32 TYR cc_start: 0.8758 (m-10) cc_final: 0.8504 (m-10) REVERT: P 81 GLU cc_start: 0.8485 (tt0) cc_final: 0.8256 (tt0) REVERT: R 86 TYR cc_start: 0.7967 (m-80) cc_final: 0.7673 (m-80) REVERT: R 100 GLN cc_start: 0.7377 (mp10) cc_final: 0.7135 (mp10) REVERT: I 588 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7388 (tpp80) REVERT: I 632 ASP cc_start: 0.9079 (t70) cc_final: 0.8657 (t0) REVERT: N 24 ARG cc_start: 0.8358 (mtp180) cc_final: 0.7919 (ttm110) REVERT: N 39 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7802 (mtmt) REVERT: N 81 GLU cc_start: 0.8013 (mp0) cc_final: 0.7810 (pm20) REVERT: K 48 ILE cc_start: 0.9019 (mt) cc_final: 0.8725 (tt) REVERT: K 72 ASP cc_start: 0.7365 (t0) cc_final: 0.6989 (p0) outliers start: 49 outliers final: 21 residues processed: 443 average time/residue: 0.1818 time to fit residues: 127.7270 Evaluate side-chains 353 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 331 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 275 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN E 195 ASN M 92 ASN J 32 ASN J 77 GLN F 195 ASN R 89 GLN N 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078153 restraints weight = 50384.571| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.12 r_work: 0.3002 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27288 Z= 0.145 Angle : 0.660 9.213 37323 Z= 0.335 Chirality : 0.044 0.298 4503 Planarity : 0.004 0.045 4503 Dihedral : 4.971 26.700 3411 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.70 % Favored : 94.81 % Rotamer: Outliers : 1.53 % Allowed : 8.84 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.34 (0.15), residues: 3105 helix: 0.77 (0.26), residues: 459 sheet: 0.98 (0.15), residues: 1119 loop : -0.48 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 103 TYR 0.015 0.001 TYR L 86 PHE 0.018 0.002 PHE J 78 TRP 0.023 0.001 TRP D 96 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27105) covalent geometry : angle 0.62452 / 0.33 (36822) SS BOND : bond 0.00328 / 0.21 ( 48) SS BOND : angle 1.03142 / 0.69 ( 96) hydrogen bonds : bond 0.04812 / 3.24 ( 1002) hydrogen bonds : angle 5.53528 / 3.88 ( 2691) link_ALPHA1-2 : bond 0.00605 / 0.34 ( 6) link_ALPHA1-2 : angle 1.82786 / 1.13 ( 18) link_ALPHA1-3 : bond 0.00647 / 0.41 ( 9) link_ALPHA1-3 : angle 1.45407 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00566 / 0.35 ( 9) link_ALPHA1-6 : angle 1.39690 / 0.93 ( 27) link_BETA1-4 : bond 0.00645 / 0.40 ( 48) link_BETA1-4 : angle 1.76810 / 1.25 ( 144) link_BETA1-6 : bond 0.00862 / 0.39 ( 3) link_BETA1-6 : angle 1.17161 / 0.66 ( 9) link_NAG-ASN : bond 0.00341 / 0.22 ( 60) link_NAG-ASN : angle 2.52696 / 1.80 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 374 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8620 (mp10) cc_final: 0.8209 (mp10) REVERT: H 72 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7396 (t70) REVERT: L 17 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6875 (mt-10) REVERT: B 588 ARG cc_start: 0.8354 (tpt170) cc_final: 0.7426 (ttm110) REVERT: B 632 ASP cc_start: 0.9154 (t70) cc_final: 0.8758 (t0) REVERT: D 24 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7824 (ptm160) REVERT: D 81 GLU cc_start: 0.7874 (mp0) cc_final: 0.7572 (pm20) REVERT: C 13 ARG cc_start: 0.6750 (mtt-85) cc_final: 0.6431 (mmt90) REVERT: C 37 ILE cc_start: 0.9182 (mm) cc_final: 0.8777 (tt) REVERT: C 48 ILE cc_start: 0.9026 (mt) cc_final: 0.8717 (tt) REVERT: O 72 ASP cc_start: 0.7623 (t0) cc_final: 0.7141 (t70) REVERT: Q 82 ASP cc_start: 0.6906 (m-30) cc_final: 0.6554 (m-30) REVERT: Q 100 GLN cc_start: 0.7544 (mp10) cc_final: 0.7340 (mp10) REVERT: G 588 ARG cc_start: 0.8302 (tpt170) cc_final: 0.7450 (ttm110) REVERT: G 632 ASP cc_start: 0.9194 (t70) cc_final: 0.8829 (t0) REVERT: M 24 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7825 (mmm-85) REVERT: M 81 GLU cc_start: 0.8080 (mp0) cc_final: 0.7820 (pm20) REVERT: F 416 LEU cc_start: 0.8787 (mt) cc_final: 0.8556 (mt) REVERT: P 32 TYR cc_start: 0.8815 (m-10) cc_final: 0.8533 (m-10) REVERT: P 46 GLU cc_start: 0.7434 (tt0) cc_final: 0.6963 (tp30) REVERT: P 72 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7556 (t70) REVERT: P 81 GLU cc_start: 0.8515 (tt0) cc_final: 0.8291 (tt0) REVERT: R 86 TYR cc_start: 0.8033 (m-80) cc_final: 0.7772 (m-80) REVERT: R 100 GLN cc_start: 0.7409 (mp10) cc_final: 0.7124 (mp10) REVERT: I 588 ARG cc_start: 0.8219 (tpt170) cc_final: 0.7478 (ttp-110) REVERT: I 632 ASP cc_start: 0.9100 (t70) cc_final: 0.8697 (t0) REVERT: N 24 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7861 (ttm110) REVERT: K 37 ILE cc_start: 0.9177 (mm) cc_final: 0.8710 (tt) REVERT: K 38 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7644 (ttm170) REVERT: K 48 ILE cc_start: 0.8980 (mt) cc_final: 0.8688 (tt) REVERT: K 86 ASP cc_start: 0.6839 (m-30) cc_final: 0.6579 (m-30) outliers start: 42 outliers final: 31 residues processed: 394 average time/residue: 0.1891 time to fit residues: 115.8791 Evaluate side-chains 371 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 338 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 261 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 162 optimal weight: 0.4980 chunk 190 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN C 77 GLN E 195 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072159 restraints weight = 51553.301| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.06 r_work: 0.2860 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27288 Z= 0.229 Angle : 0.704 9.423 37323 Z= 0.352 Chirality : 0.046 0.296 4503 Planarity : 0.004 0.048 4503 Dihedral : 5.033 28.621 3411 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.12 % Favored : 94.40 % Rotamer: Outliers : 2.18 % Allowed : 9.10 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.04 (0.15), residues: 3105 helix: 0.60 (0.26), residues: 459 sheet: 0.84 (0.15), residues: 1131 loop : -0.76 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 103 TYR 0.016 0.002 TYR J 50 PHE 0.026 0.002 PHE C 78 TRP 0.024 0.002 TRP M 96 HIS 0.008 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (27105) covalent geometry : angle 0.67108 / 0.35 (36822) SS BOND : bond 0.00416 / 0.23 ( 48) SS BOND : angle 1.31840 / 0.84 ( 96) hydrogen bonds : bond 0.05005 / 3.37 ( 1002) hydrogen bonds : angle 5.41745 / 3.79 ( 2691) link_ALPHA1-2 : bond 0.00429 / 0.24 ( 6) link_ALPHA1-2 : angle 1.90147 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00422 / 0.27 ( 9) link_ALPHA1-3 : angle 1.49171 / 1.01 ( 27) link_ALPHA1-6 : bond 0.00368 / 0.22 ( 9) link_ALPHA1-6 : angle 1.52809 / 1.03 ( 27) link_BETA1-4 : bond 0.00458 / 0.27 ( 48) link_BETA1-4 : angle 1.70592 / 1.20 ( 144) link_BETA1-6 : bond 0.00655 / 0.29 ( 3) link_BETA1-6 : angle 1.13177 / 0.64 ( 9) link_NAG-ASN : bond 0.00358 / 0.25 ( 60) link_NAG-ASN : angle 2.52533 / 1.80 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8659 (mp10) cc_final: 0.8291 (mp10) REVERT: L 83 PHE cc_start: 0.6172 (m-80) cc_final: 0.5878 (m-80) REVERT: B 588 ARG cc_start: 0.8456 (tpt170) cc_final: 0.7648 (ttm110) REVERT: B 632 ASP cc_start: 0.9239 (t70) cc_final: 0.8841 (t0) REVERT: D 81 GLU cc_start: 0.7938 (mp0) cc_final: 0.7658 (pm20) REVERT: C 13 ARG cc_start: 0.6908 (mtt-85) cc_final: 0.6650 (mmt90) REVERT: C 37 ILE cc_start: 0.9163 (mm) cc_final: 0.8732 (tt) REVERT: C 66 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7375 (mtm110) REVERT: O 11 PHE cc_start: 0.7197 (m-80) cc_final: 0.6825 (m-80) REVERT: Q 82 ASP cc_start: 0.7057 (m-30) cc_final: 0.6797 (m-30) REVERT: G 588 ARG cc_start: 0.8412 (tpt170) cc_final: 0.7578 (ttm110) REVERT: G 632 ASP cc_start: 0.9204 (t70) cc_final: 0.8850 (t0) REVERT: M 24 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7827 (mmm-85) REVERT: M 81 GLU cc_start: 0.8064 (mp0) cc_final: 0.7832 (pm20) REVERT: F 416 LEU cc_start: 0.9033 (mt) cc_final: 0.8800 (mt) REVERT: P 32 TYR cc_start: 0.8932 (m-10) cc_final: 0.8651 (m-10) REVERT: P 46 GLU cc_start: 0.7583 (tt0) cc_final: 0.7166 (tp30) REVERT: P 72 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7732 (t70) REVERT: P 81 GLU cc_start: 0.8569 (tt0) cc_final: 0.8366 (tt0) REVERT: R 82 ASP cc_start: 0.7270 (m-30) cc_final: 0.7021 (m-30) REVERT: I 588 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7645 (ttp-110) REVERT: I 632 ASP cc_start: 0.9135 (t70) cc_final: 0.8776 (t0) REVERT: N 24 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7822 (ttm-80) REVERT: N 93 ASP cc_start: 0.8345 (t0) cc_final: 0.7646 (p0) outliers start: 60 outliers final: 50 residues processed: 382 average time/residue: 0.1880 time to fit residues: 113.8814 Evaluate side-chains 385 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 548 ILE Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 195 ASN Q 89 GLN M 92 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.106299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073695 restraints weight = 51315.597| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.40 r_work: 0.2848 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27288 Z= 0.162 Angle : 0.647 9.481 37323 Z= 0.321 Chirality : 0.044 0.299 4503 Planarity : 0.004 0.047 4503 Dihedral : 4.896 28.349 3411 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.12 % Favored : 94.49 % Rotamer: Outliers : 1.93 % Allowed : 10.26 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.04 (0.15), residues: 3105 helix: 0.57 (0.26), residues: 477 sheet: 0.94 (0.16), residues: 1122 loop : -0.86 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 103 TYR 0.014 0.001 TYR J 50 PHE 0.018 0.002 PHE J 78 TRP 0.024 0.001 TRP N 96 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (27105) covalent geometry : angle 0.61591 / 0.31 (36822) SS BOND : bond 0.00362 / 0.21 ( 48) SS BOND : angle 1.11044 / 0.74 ( 96) hydrogen bonds : bond 0.04518 / 3.03 ( 1002) hydrogen bonds : angle 5.21696 / 3.65 ( 2691) link_ALPHA1-2 : bond 0.00451 / 0.25 ( 6) link_ALPHA1-2 : angle 1.79104 / 1.11 ( 18) link_ALPHA1-3 : bond 0.00454 / 0.29 ( 9) link_ALPHA1-3 : angle 1.44040 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00389 / 0.24 ( 9) link_ALPHA1-6 : angle 1.41103 / 0.95 ( 27) link_BETA1-4 : bond 0.00452 / 0.27 ( 48) link_BETA1-4 : angle 1.46283 / 1.03 ( 144) link_BETA1-6 : bond 0.00313 / 0.13 ( 3) link_BETA1-6 : angle 1.11821 / 0.64 ( 9) link_NAG-ASN : bond 0.00311 / 0.21 ( 60) link_NAG-ASN : angle 2.39284 / 1.70 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8660 (mp10) cc_final: 0.8283 (mp10) REVERT: H 11 PHE cc_start: 0.7179 (m-80) cc_final: 0.6822 (m-80) REVERT: H 82 ASN cc_start: 0.6672 (t0) cc_final: 0.6395 (t0) REVERT: B 588 ARG cc_start: 0.8456 (tpt170) cc_final: 0.7603 (ttm110) REVERT: B 632 ASP cc_start: 0.9296 (t70) cc_final: 0.8903 (t0) REVERT: D 24 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7859 (mmm-85) REVERT: D 81 GLU cc_start: 0.8005 (mp0) cc_final: 0.7698 (pm20) REVERT: C 37 ILE cc_start: 0.9124 (mm) cc_final: 0.8687 (tt) REVERT: C 38 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7333 (ttm-80) REVERT: C 66 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7389 (mtm110) REVERT: C 86 ASP cc_start: 0.7243 (m-30) cc_final: 0.6979 (m-30) REVERT: O 11 PHE cc_start: 0.7054 (m-80) cc_final: 0.6800 (m-80) REVERT: O 46 GLU cc_start: 0.7571 (tt0) cc_final: 0.7292 (tp30) REVERT: O 72 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7241 (t70) REVERT: Q 76 ARG cc_start: 0.7393 (mmt180) cc_final: 0.7125 (mmm-85) REVERT: Q 82 ASP cc_start: 0.6895 (m-30) cc_final: 0.6630 (m-30) REVERT: G 563 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7293 (pt0) REVERT: G 588 ARG cc_start: 0.8404 (tpt170) cc_final: 0.7552 (ttm110) REVERT: G 632 ASP cc_start: 0.9239 (t70) cc_final: 0.8883 (t0) REVERT: M 81 GLU cc_start: 0.7972 (mp0) cc_final: 0.7698 (pm20) REVERT: J 53 ARG cc_start: 0.8511 (mpp80) cc_final: 0.8259 (mmt90) REVERT: F 416 LEU cc_start: 0.9005 (mt) cc_final: 0.8742 (mt) REVERT: P 32 TYR cc_start: 0.8977 (m-10) cc_final: 0.8690 (m-10) REVERT: P 46 GLU cc_start: 0.7638 (tt0) cc_final: 0.7188 (tp30) REVERT: P 72 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7703 (t70) REVERT: I 588 ARG cc_start: 0.8340 (tpt170) cc_final: 0.7627 (ttp-110) REVERT: I 632 ASP cc_start: 0.9206 (t70) cc_final: 0.8863 (t0) REVERT: N 24 ARG cc_start: 0.8360 (mtp180) cc_final: 0.7758 (ttm-80) REVERT: N 79 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7839 (tt0) REVERT: N 81 GLU cc_start: 0.7635 (pm20) cc_final: 0.7137 (pm20) REVERT: N 105 GLU cc_start: 0.7315 (pp20) cc_final: 0.7018 (pp20) outliers start: 53 outliers final: 40 residues processed: 383 average time/residue: 0.1857 time to fit residues: 111.3896 Evaluate side-chains 374 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 332 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 240 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068379 restraints weight = 52106.057| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.09 r_work: 0.2788 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 27288 Z= 0.346 Angle : 0.817 12.056 37323 Z= 0.402 Chirality : 0.049 0.300 4503 Planarity : 0.005 0.052 4503 Dihedral : 5.397 30.756 3411 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.54 % Favored : 92.95 % Rotamer: Outliers : 2.66 % Allowed : 10.52 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3105 helix: 0.01 (0.25), residues: 477 sheet: 0.80 (0.16), residues: 1110 loop : -1.16 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 103 TYR 0.020 0.002 TYR J 50 PHE 0.022 0.003 PHE E 53 TRP 0.036 0.003 TRP D 96 HIS 0.010 0.002 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.35 (27105) covalent geometry : angle 0.78645 / 0.40 (36822) SS BOND : bond 0.00587 / 0.32 ( 48) SS BOND : angle 1.52327 / 1.04 ( 96) hydrogen bonds : bond 0.05603 / 3.77 ( 1002) hydrogen bonds : angle 5.49244 / 3.84 ( 2691) link_ALPHA1-2 : bond 0.00388 / 0.22 ( 6) link_ALPHA1-2 : angle 2.07414 / 1.30 ( 18) link_ALPHA1-3 : bond 0.00242 / 0.16 ( 9) link_ALPHA1-3 : angle 1.78478 / 1.19 ( 27) link_ALPHA1-6 : bond 0.00364 / 0.22 ( 9) link_ALPHA1-6 : angle 1.66997 / 1.11 ( 27) link_BETA1-4 : bond 0.00410 / 0.23 ( 48) link_BETA1-4 : angle 1.69569 / 1.18 ( 144) link_BETA1-6 : bond 0.00713 / 0.32 ( 3) link_BETA1-6 : angle 1.11926 / 0.62 ( 9) link_NAG-ASN : bond 0.00588 / 0.41 ( 60) link_NAG-ASN : angle 2.66619 / 1.90 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 338 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8143 (tpp) cc_final: 0.7865 (mtm) REVERT: H 11 PHE cc_start: 0.7238 (m-80) cc_final: 0.6871 (m-80) REVERT: H 46 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: H 62 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8426 (ttmt) REVERT: L 61 ARG cc_start: 0.6458 (mtp180) cc_final: 0.6028 (mtp180) REVERT: B 632 ASP cc_start: 0.9280 (t70) cc_final: 0.8921 (t0) REVERT: D 81 GLU cc_start: 0.8103 (mp0) cc_final: 0.7769 (pm20) REVERT: C 13 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6851 (mmt90) REVERT: C 37 ILE cc_start: 0.9135 (mm) cc_final: 0.8735 (tt) REVERT: O 72 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7491 (t70) REVERT: Q 17 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7305 (mt-10) REVERT: Q 76 ARG cc_start: 0.7440 (mmt180) cc_final: 0.7136 (mmm-85) REVERT: Q 82 ASP cc_start: 0.7075 (m-30) cc_final: 0.6798 (m-30) REVERT: G 588 ARG cc_start: 0.8422 (tpt170) cc_final: 0.7676 (ttm110) REVERT: G 632 ASP cc_start: 0.9226 (t70) cc_final: 0.8886 (t0) REVERT: M 81 GLU cc_start: 0.8058 (mp0) cc_final: 0.7803 (pm20) REVERT: J 13 ARG cc_start: 0.6592 (mmt90) cc_final: 0.6312 (mpp-170) REVERT: F 425 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8056 (t0) REVERT: P 46 GLU cc_start: 0.7922 (tt0) cc_final: 0.7467 (tp30) REVERT: P 72 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7732 (t70) REVERT: I 588 ARG cc_start: 0.8351 (tpt170) cc_final: 0.7621 (ttp-110) REVERT: I 632 ASP cc_start: 0.9154 (t70) cc_final: 0.8787 (t0) REVERT: N 24 ARG cc_start: 0.8379 (mtp180) cc_final: 0.7810 (ttm110) REVERT: N 93 ASP cc_start: 0.8301 (t0) cc_final: 0.8015 (m-30) REVERT: K 37 ILE cc_start: 0.9216 (mm) cc_final: 0.8716 (tt) REVERT: K 52 ASN cc_start: 0.8435 (t0) cc_final: 0.8192 (t0) outliers start: 73 outliers final: 58 residues processed: 386 average time/residue: 0.1903 time to fit residues: 115.1425 Evaluate side-chains 374 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 548 ILE Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 176 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072824 restraints weight = 51107.285| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.02 r_work: 0.2874 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27288 Z= 0.120 Angle : 0.635 9.832 37323 Z= 0.315 Chirality : 0.043 0.299 4503 Planarity : 0.004 0.048 4503 Dihedral : 5.002 28.516 3411 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.54 % Favored : 94.24 % Rotamer: Outliers : 1.27 % Allowed : 12.70 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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 (0.15), residues: 3105 helix: 0.52 (0.26), residues: 480 sheet: 0.93 (0.16), residues: 1110 loop : -1.09 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 103 TYR 0.011 0.001 TYR K 50 PHE 0.012 0.001 PHE C 100C TRP 0.026 0.001 TRP D 96 HIS 0.005 0.001 HIS P 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (27105) covalent geometry : angle 0.60470 / 0.31 (36822) SS BOND : bond 0.00303 / 0.19 ( 48) SS BOND : angle 1.10060 / 0.75 ( 96) hydrogen bonds : bond 0.04257 / 2.84 ( 1002) hydrogen bonds : angle 5.13536 / 3.59 ( 2691) link_ALPHA1-2 : bond 0.00412 / 0.23 ( 6) link_ALPHA1-2 : angle 1.75414 / 1.08 ( 18) link_ALPHA1-3 : bond 0.00485 / 0.31 ( 9) link_ALPHA1-3 : angle 1.43796 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00453 / 0.28 ( 9) link_ALPHA1-6 : angle 1.36815 / 0.91 ( 27) link_BETA1-4 : bond 0.00446 / 0.26 ( 48) link_BETA1-4 : angle 1.31217 / 0.93 ( 144) link_BETA1-6 : bond 0.00453 / 0.21 ( 3) link_BETA1-6 : angle 1.13567 / 0.66 ( 9) link_NAG-ASN : bond 0.00305 / 0.20 ( 60) link_NAG-ASN : angle 2.38798 / 1.70 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 355 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7967 (tpp) cc_final: 0.7747 (mtm) REVERT: H 11 PHE cc_start: 0.7085 (m-80) cc_final: 0.6869 (m-80) REVERT: L 61 ARG cc_start: 0.6576 (mtp180) cc_final: 0.6252 (mtp180) REVERT: B 588 ARG cc_start: 0.8432 (tpt170) cc_final: 0.7625 (ttm110) REVERT: B 632 ASP cc_start: 0.9274 (t70) cc_final: 0.8853 (t0) REVERT: D 24 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7823 (mmm-85) REVERT: D 81 GLU cc_start: 0.8124 (mp0) cc_final: 0.7832 (pm20) REVERT: C 13 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6692 (mmt90) REVERT: C 37 ILE cc_start: 0.9088 (mm) cc_final: 0.8648 (tt) REVERT: C 38 ARG cc_start: 0.7840 (ttm170) cc_final: 0.7499 (ttm-80) REVERT: E 122 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7978 (pp) REVERT: E 150 MET cc_start: 0.8583 (mmm) cc_final: 0.8324 (mmt) REVERT: O 72 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7179 (t70) REVERT: Q 27 GLN cc_start: 0.7404 (mt0) cc_final: 0.6887 (tt0) REVERT: Q 76 ARG cc_start: 0.7318 (mmt180) cc_final: 0.7078 (mmm-85) REVERT: Q 82 ASP cc_start: 0.7106 (m-30) cc_final: 0.6763 (m-30) REVERT: G 563 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7406 (pt0) REVERT: G 588 ARG cc_start: 0.8386 (tpt170) cc_final: 0.7587 (ttm110) REVERT: G 632 ASP cc_start: 0.9202 (t70) cc_final: 0.8838 (t0) REVERT: M 81 GLU cc_start: 0.8088 (mp0) cc_final: 0.7815 (pm20) REVERT: J 53 ARG cc_start: 0.8717 (mpp80) cc_final: 0.8333 (mmt90) REVERT: F 122 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7894 (pp) REVERT: F 416 LEU cc_start: 0.9029 (mt) cc_final: 0.8792 (mt) REVERT: P 32 TYR cc_start: 0.8953 (m-80) cc_final: 0.8628 (m-10) REVERT: R 61 ARG cc_start: 0.6180 (mtp180) cc_final: 0.5829 (mtp180) REVERT: R 82 ASP cc_start: 0.7090 (m-30) cc_final: 0.6832 (m-30) REVERT: I 588 ARG cc_start: 0.8300 (tpt170) cc_final: 0.7631 (ttp-110) REVERT: I 632 ASP cc_start: 0.9096 (t70) cc_final: 0.8749 (t0) REVERT: N 24 ARG cc_start: 0.8338 (mtp180) cc_final: 0.7728 (ttm-80) REVERT: N 105 GLU cc_start: 0.7390 (pp20) cc_final: 0.7117 (pp20) REVERT: K 37 ILE cc_start: 0.9172 (mm) cc_final: 0.8627 (tt) outliers start: 35 outliers final: 23 residues processed: 373 average time/residue: 0.1919 time to fit residues: 111.6381 Evaluate side-chains 351 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 325 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 262 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073576 restraints weight = 51480.728| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.03 r_work: 0.2891 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27288 Z= 0.115 Angle : 0.616 9.614 37323 Z= 0.305 Chirality : 0.043 0.301 4503 Planarity : 0.004 0.050 4503 Dihedral : 4.816 27.199 3411 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 0.98 % Allowed : 13.17 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 3105 helix: 0.83 (0.26), residues: 480 sheet: 1.00 (0.16), residues: 1092 loop : -1.07 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.012 0.001 TYR K 50 PHE 0.021 0.001 PHE H 63 TRP 0.024 0.001 TRP N 94 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (27105) covalent geometry : angle 0.58887 / 0.30 (36822) SS BOND : bond 0.00270 / 0.17 ( 48) SS BOND : angle 0.93174 / 0.63 ( 96) hydrogen bonds : bond 0.03954 / 2.63 ( 1002) hydrogen bonds : angle 4.97871 / 3.49 ( 2691) link_ALPHA1-2 : bond 0.00419 / 0.23 ( 6) link_ALPHA1-2 : angle 1.65366 / 1.02 ( 18) link_ALPHA1-3 : bond 0.00474 / 0.30 ( 9) link_ALPHA1-3 : angle 1.43949 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00399 / 0.25 ( 9) link_ALPHA1-6 : angle 1.37485 / 0.92 ( 27) link_BETA1-4 : bond 0.00441 / 0.26 ( 48) link_BETA1-4 : angle 1.27202 / 0.90 ( 144) link_BETA1-6 : bond 0.00337 / 0.15 ( 3) link_BETA1-6 : angle 1.15659 / 0.66 ( 9) link_NAG-ASN : bond 0.00300 / 0.20 ( 60) link_NAG-ASN : angle 2.25711 / 1.61 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7931 (tpp) cc_final: 0.7730 (mtm) REVERT: H 11 PHE cc_start: 0.7044 (m-80) cc_final: 0.6751 (m-80) REVERT: H 46 GLU cc_start: 0.7379 (tp30) cc_final: 0.6411 (tt0) REVERT: L 27 GLN cc_start: 0.7313 (mt0) cc_final: 0.6689 (tt0) REVERT: L 61 ARG cc_start: 0.6498 (mtp180) cc_final: 0.5994 (mtp180) REVERT: B 588 ARG cc_start: 0.8419 (tpt170) cc_final: 0.7611 (ttm110) REVERT: B 632 ASP cc_start: 0.9271 (t70) cc_final: 0.8871 (t0) REVERT: D 24 ARG cc_start: 0.8150 (mtp180) cc_final: 0.7844 (ptm160) REVERT: D 81 GLU cc_start: 0.8105 (mp0) cc_final: 0.7816 (pm20) REVERT: C 13 ARG cc_start: 0.6992 (mtt-85) cc_final: 0.6646 (mmt90) REVERT: C 37 ILE cc_start: 0.9092 (mm) cc_final: 0.8663 (tt) REVERT: E 150 MET cc_start: 0.8597 (mmm) cc_final: 0.8364 (mmt) REVERT: O 72 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7165 (t70) REVERT: Q 17 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7359 (mp0) REVERT: Q 61 ARG cc_start: 0.5923 (mtm180) cc_final: 0.5586 (mtp180) REVERT: Q 82 ASP cc_start: 0.7137 (m-30) cc_final: 0.6699 (m-30) REVERT: G 563 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7503 (pt0) REVERT: G 588 ARG cc_start: 0.8384 (tpt170) cc_final: 0.7580 (ttm110) REVERT: G 632 ASP cc_start: 0.9195 (t70) cc_final: 0.8839 (t0) REVERT: M 81 GLU cc_start: 0.8028 (mp0) cc_final: 0.7782 (pm20) REVERT: J 16 GLU cc_start: 0.6466 (pt0) cc_final: 0.6241 (pm20) REVERT: J 53 ARG cc_start: 0.8744 (mpp80) cc_final: 0.8382 (mmt90) REVERT: F 416 LEU cc_start: 0.8951 (mt) cc_final: 0.8667 (mt) REVERT: P 32 TYR cc_start: 0.8912 (m-80) cc_final: 0.8546 (m-10) REVERT: R 61 ARG cc_start: 0.6274 (mtp180) cc_final: 0.6028 (mtp180) REVERT: I 530 MET cc_start: 0.8745 (mmm) cc_final: 0.8113 (mtt) REVERT: I 588 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7642 (ttp-110) REVERT: I 632 ASP cc_start: 0.9159 (t70) cc_final: 0.8795 (t0) REVERT: N 24 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7712 (ttm-80) REVERT: N 105 GLU cc_start: 0.7257 (pp20) cc_final: 0.6947 (pp20) outliers start: 27 outliers final: 25 residues processed: 359 average time/residue: 0.1850 time to fit residues: 103.4708 Evaluate side-chains 356 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 1.9990 chunk 186 optimal weight: 0.0370 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** 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 = 0.3558 r_free = 0.3558 target = 0.105495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072369 restraints weight = 51726.513| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.03 r_work: 0.2867 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27288 Z= 0.155 Angle : 0.638 9.588 37323 Z= 0.315 Chirality : 0.044 0.301 4503 Planarity : 0.004 0.050 4503 Dihedral : 4.821 27.530 3411 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.85 % Rotamer: Outliers : 1.06 % Allowed : 13.72 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.05 (0.16), residues: 3105 helix: 0.97 (0.26), residues: 462 sheet: 0.89 (0.16), residues: 1128 loop : -1.10 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.018 0.001 TYR L 87 PHE 0.017 0.002 PHE H 63 TRP 0.032 0.001 TRP D 96 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (27105) covalent geometry : angle 0.61140 / 0.31 (36822) SS BOND : bond 0.00274 / 0.16 ( 48) SS BOND : angle 0.98460 / 0.66 ( 96) hydrogen bonds : bond 0.04159 / 2.78 ( 1002) hydrogen bonds : angle 4.97460 / 3.48 ( 2691) link_ALPHA1-2 : bond 0.00389 / 0.22 ( 6) link_ALPHA1-2 : angle 1.71961 / 1.06 ( 18) link_ALPHA1-3 : bond 0.00408 / 0.26 ( 9) link_ALPHA1-3 : angle 1.48211 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00315 / 0.19 ( 9) link_ALPHA1-6 : angle 1.40996 / 0.93 ( 27) link_BETA1-4 : bond 0.00415 / 0.24 ( 48) link_BETA1-4 : angle 1.31143 / 0.92 ( 144) link_BETA1-6 : bond 0.00314 / 0.14 ( 3) link_BETA1-6 : angle 1.11669 / 0.63 ( 9) link_NAG-ASN : bond 0.00303 / 0.21 ( 60) link_NAG-ASN : angle 2.25286 / 1.61 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.7952 (tpp) cc_final: 0.7690 (mtm) REVERT: H 11 PHE cc_start: 0.6974 (m-80) cc_final: 0.6648 (m-80) REVERT: L 27 GLN cc_start: 0.7233 (mt0) cc_final: 0.6602 (tt0) REVERT: L 61 ARG cc_start: 0.6428 (mtp180) cc_final: 0.5881 (mtp180) REVERT: B 588 ARG cc_start: 0.8435 (tpt170) cc_final: 0.7627 (ttm110) REVERT: B 632 ASP cc_start: 0.9307 (t70) cc_final: 0.8922 (t0) REVERT: D 24 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7865 (ptm160) REVERT: D 81 GLU cc_start: 0.8126 (mp0) cc_final: 0.7809 (pm20) REVERT: C 13 ARG cc_start: 0.6962 (mtt-85) cc_final: 0.6556 (mmt90) REVERT: C 37 ILE cc_start: 0.9005 (mm) cc_final: 0.8560 (tt) REVERT: E 150 MET cc_start: 0.8590 (mmm) cc_final: 0.8351 (mmt) REVERT: O 46 GLU cc_start: 0.7603 (tt0) cc_final: 0.7270 (tp30) REVERT: O 72 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7206 (t70) REVERT: Q 17 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7336 (mt-10) REVERT: Q 61 ARG cc_start: 0.5932 (mtm180) cc_final: 0.5570 (mtp180) REVERT: Q 82 ASP cc_start: 0.7174 (m-30) cc_final: 0.6757 (m-30) REVERT: G 563 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7522 (pt0) REVERT: G 588 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7600 (ttm110) REVERT: G 632 ASP cc_start: 0.9209 (t70) cc_final: 0.8859 (t0) REVERT: M 81 GLU cc_start: 0.8045 (mp0) cc_final: 0.7798 (pm20) REVERT: J 16 GLU cc_start: 0.6614 (pt0) cc_final: 0.6411 (pm20) REVERT: J 53 ARG cc_start: 0.8774 (mpp80) cc_final: 0.8389 (mmt90) REVERT: P 32 TYR cc_start: 0.8944 (m-80) cc_final: 0.8543 (m-10) REVERT: R 61 ARG cc_start: 0.6283 (mtp180) cc_final: 0.6055 (mtp180) REVERT: I 530 MET cc_start: 0.8856 (mmm) cc_final: 0.8306 (mtt) REVERT: I 588 ARG cc_start: 0.8321 (tpt170) cc_final: 0.7652 (ttp-110) REVERT: I 632 ASP cc_start: 0.9198 (t70) cc_final: 0.8845 (t0) REVERT: N 24 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7728 (ttm-80) REVERT: N 105 GLU cc_start: 0.7244 (pp20) cc_final: 0.6925 (pp20) outliers start: 29 outliers final: 27 residues processed: 350 average time/residue: 0.1843 time to fit residues: 100.1727 Evaluate side-chains 352 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** 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 = 0.3565 r_free = 0.3565 target = 0.105934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072892 restraints weight = 51432.652| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.02 r_work: 0.2877 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27288 Z= 0.138 Angle : 0.624 9.561 37323 Z= 0.309 Chirality : 0.043 0.299 4503 Planarity : 0.004 0.051 4503 Dihedral : 4.789 27.499 3411 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 0.95 % Allowed : 13.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 3105 helix: 1.05 (0.26), residues: 462 sheet: 0.96 (0.16), residues: 1116 loop : -1.13 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.014 0.001 TYR L 87 PHE 0.016 0.001 PHE H 63 TRP 0.032 0.001 TRP N 94 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (27105) covalent geometry : angle 0.59783 / 0.30 (36822) SS BOND : bond 0.00262 / 0.16 ( 48) SS BOND : angle 0.97600 / 0.66 ( 96) hydrogen bonds : bond 0.04048 / 2.70 ( 1002) hydrogen bonds : angle 4.93420 / 3.45 ( 2691) link_ALPHA1-2 : bond 0.00385 / 0.21 ( 6) link_ALPHA1-2 : angle 1.68710 / 1.04 ( 18) link_ALPHA1-3 : bond 0.00427 / 0.27 ( 9) link_ALPHA1-3 : angle 1.46326 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00335 / 0.21 ( 9) link_ALPHA1-6 : angle 1.38654 / 0.92 ( 27) link_BETA1-4 : bond 0.00410 / 0.24 ( 48) link_BETA1-4 : angle 1.26623 / 0.89 ( 144) link_BETA1-6 : bond 0.00289 / 0.13 ( 3) link_BETA1-6 : angle 1.13965 / 0.65 ( 9) link_NAG-ASN : bond 0.00296 / 0.20 ( 60) link_NAG-ASN : angle 2.21371 / 1.58 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.7944 (tpp) cc_final: 0.7675 (mtm) REVERT: H 11 PHE cc_start: 0.6990 (m-80) cc_final: 0.6613 (m-80) REVERT: H 46 GLU cc_start: 0.7355 (tp30) cc_final: 0.6388 (tt0) REVERT: H 57 MET cc_start: 0.9203 (ttp) cc_final: 0.8939 (ttp) REVERT: L 27 GLN cc_start: 0.7436 (mt0) cc_final: 0.6973 (tt0) REVERT: L 61 ARG cc_start: 0.6461 (mtp180) cc_final: 0.5839 (mtp180) REVERT: L 83 PHE cc_start: 0.5872 (m-80) cc_final: 0.5470 (m-80) REVERT: B 588 ARG cc_start: 0.8436 (tpt170) cc_final: 0.7620 (ttm110) REVERT: B 632 ASP cc_start: 0.9304 (t70) cc_final: 0.8918 (t0) REVERT: D 81 GLU cc_start: 0.8123 (mp0) cc_final: 0.7837 (pm20) REVERT: C 37 ILE cc_start: 0.9033 (mm) cc_final: 0.8573 (tt) REVERT: E 150 MET cc_start: 0.8550 (mmm) cc_final: 0.8317 (mmt) REVERT: O 46 GLU cc_start: 0.7584 (tt0) cc_final: 0.7252 (tp30) REVERT: O 72 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7181 (t70) REVERT: Q 17 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7262 (mt-10) REVERT: Q 61 ARG cc_start: 0.5949 (mtm180) cc_final: 0.5587 (mtp180) REVERT: Q 82 ASP cc_start: 0.7151 (m-30) cc_final: 0.6754 (m-30) REVERT: G 563 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7557 (pt0) REVERT: G 588 ARG cc_start: 0.8401 (tpt170) cc_final: 0.7590 (ttm110) REVERT: G 632 ASP cc_start: 0.9208 (t70) cc_final: 0.8870 (t0) REVERT: M 81 GLU cc_start: 0.8073 (mp0) cc_final: 0.7791 (pm20) REVERT: J 53 ARG cc_start: 0.8767 (mpp80) cc_final: 0.8372 (mmt90) REVERT: P 46 GLU cc_start: 0.7427 (tp30) cc_final: 0.6666 (tt0) REVERT: R 61 ARG cc_start: 0.6190 (mtp180) cc_final: 0.5974 (mtp180) REVERT: I 530 MET cc_start: 0.8847 (mmm) cc_final: 0.8382 (mtp) REVERT: I 588 ARG cc_start: 0.8313 (tpt170) cc_final: 0.7643 (ttp-110) REVERT: I 632 ASP cc_start: 0.9200 (t70) cc_final: 0.8864 (t0) REVERT: N 24 ARG cc_start: 0.8347 (mtp180) cc_final: 0.7719 (ttm-80) outliers start: 26 outliers final: 25 residues processed: 348 average time/residue: 0.1802 time to fit residues: 97.4380 Evaluate side-chains 351 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 325 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 157 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 169 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.106498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073511 restraints weight = 51165.271| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.02 r_work: 0.2888 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27288 Z= 0.124 Angle : 0.613 9.485 37323 Z= 0.304 Chirality : 0.043 0.296 4503 Planarity : 0.004 0.052 4503 Dihedral : 4.727 27.649 3411 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.99 % Favored : 93.82 % Rotamer: Outliers : 1.13 % Allowed : 13.90 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.00 (0.16), residues: 3105 helix: 1.04 (0.26), residues: 468 sheet: 0.96 (0.16), residues: 1119 loop : -1.11 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 103 TYR 0.014 0.001 TYR L 87 PHE 0.016 0.001 PHE P 63 TRP 0.031 0.001 TRP N 94 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (27105) covalent geometry : angle 0.58797 / 0.30 (36822) SS BOND : bond 0.00241 / 0.15 ( 48) SS BOND : angle 0.94159 / 0.63 ( 96) hydrogen bonds : bond 0.03905 / 2.61 ( 1002) hydrogen bonds : angle 4.89559 / 3.42 ( 2691) link_ALPHA1-2 : bond 0.00387 / 0.22 ( 6) link_ALPHA1-2 : angle 1.65231 / 1.02 ( 18) link_ALPHA1-3 : bond 0.00447 / 0.28 ( 9) link_ALPHA1-3 : angle 1.44606 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00354 / 0.22 ( 9) link_ALPHA1-6 : angle 1.37604 / 0.91 ( 27) link_BETA1-4 : bond 0.00409 / 0.24 ( 48) link_BETA1-4 : angle 1.22929 / 0.86 ( 144) link_BETA1-6 : bond 0.00281 / 0.12 ( 3) link_BETA1-6 : angle 1.15552 / 0.65 ( 9) link_NAG-ASN : bond 0.00297 / 0.20 ( 60) link_NAG-ASN : angle 2.16632 / 1.55 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.55 seconds wall clock time: 119 minutes 44.54 seconds (7184.54 seconds total)