Starting phenix.real_space_refine on Fri Mar 6 08:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.map" model { file = "/net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxd_24071/03_2026/7mxd_24071.cif" } resolution = 3.4 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 145 5.16 5 C 18502 2.51 5 N 4835 2.21 5 O 6011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29496 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "G" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "U" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "X" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 122 Unusual residues: {'NAG': 8, 'PO4': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.64, per 1000 atoms: 0.23 Number of scatterers: 29496 At special positions: 0 Unit cell: (174.08, 172.72, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 145 16.00 P 3 15.00 O 6011 8.00 N 4835 7.00 C 18502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 140 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS Y 214 " distance=2.03 Simple disulfide: pdb=" SG CYS X 152 " - pdb=" SG CYS X 208 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA o 3 " - " MAN o 6 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 149 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 405 " " NAG A 608 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG D 301 " - " ASN D 72 " " NAG E 1 " - " ASN A 156 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 149 " " NAG F 608 " - " ASN F 355 " " NAG F 609 " - " ASN F 405 " " NAG F 610 " - " ASN F 339 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 149 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 339 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 637 " " NAG H 703 " - " ASN H 625 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 616 " " NAG K 301 " - " ASN K 72 " " NAG L 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN A 334 " " NAG W 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN I 625 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 448 " " NAG i 1 " - " ASN F 88 " " NAG j 1 " - " ASN F 334 " " NAG k 1 " - " ASN F 241 " " NAG l 1 " - " ASN F 289 " " NAG m 1 " - " ASN F 160 " " NAG n 1 " - " ASN G 156 " " NAG o 1 " - " ASN G 262 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 386 " " NAG s 1 " - " ASN G 448 " " NAG t 1 " - " ASN G 88 " " NAG u 1 " - " ASN G 334 " " NAG v 1 " - " ASN G 241 " " NAG w 1 " - " ASN G 289 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 78 sheets defined 14.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.221A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.573A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.233A pdb=" N GLU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.560A pdb=" N ASP A 477 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.607A pdb=" N ASP C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.521A pdb=" N ASP C 86 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.716A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.552A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.390A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.712A pdb=" N LYS F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.605A pdb=" N ASP F 477 " --> pdb=" O ASN F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.520A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.986A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.619A pdb=" N MET G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.608A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.662A pdb=" N ASP J 31 " --> pdb=" O ASN J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.820A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.011A pdb=" N ILE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.766A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.588A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASP S 31 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.921A pdb=" N THR S 87 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.903A pdb=" N ILE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 126 removed outlier: 3.749A pdb=" N LEU U 125 " --> pdb=" O SER U 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS U 126 " --> pdb=" O ASP U 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 121 through 126' Processing helix chain 'U' and resid 182 through 189 removed outlier: 3.635A pdb=" N TYR U 186 " --> pdb=" O SER U 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 188 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 182 through 189' Processing helix chain 'X' and resid 61 through 65 Processing helix chain 'Y' and resid 121 through 125 Processing helix chain 'Y' and resid 182 through 187 removed outlier: 3.838A pdb=" N GLN Y 187 " --> pdb=" O ASN Y 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.896A pdb=" N ASN B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.929A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.517A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 597 removed outlier: 4.098A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.952A pdb=" N ASP B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.014A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 551 removed outlier: 4.028A pdb=" N GLN I 550 " --> pdb=" O GLY I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 568 Processing helix chain 'I' and resid 569 through 597 removed outlier: 3.606A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE I 592 " --> pdb=" O GLU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.943A pdb=" N ASN I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 659 removed outlier: 4.069A pdb=" N ASP I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP I 659 " --> pdb=" O ILE I 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 547 through 551 removed outlier: 3.759A pdb=" N GLN H 550 " --> pdb=" O GLY H 547 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 568 Processing helix chain 'H' and resid 569 through 597 removed outlier: 3.611A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 575 " --> pdb=" O TRP H 571 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 576 " --> pdb=" O GLY H 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA H 582 " --> pdb=" O ALA H 578 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 589 " --> pdb=" O ARG H 585 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE H 592 " --> pdb=" O GLU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 624 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 659 removed outlier: 4.071A pdb=" N ASP H 644 " --> pdb=" O SER H 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.334A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.859A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 284 through 312 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 271 through 274 current: chain 'A' and resid 441 through 456 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.614A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 414 through 421 removed outlier: 4.555A pdb=" N ASN A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE A 294 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ASN A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.193A pdb=" N CYS A 296 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N LYS A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.737A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.218A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.542A pdb=" N ASP D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.566A pdb=" N TYR D 49 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.601A pdb=" N LEU D 135 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.234A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.005A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.623A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.822A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 130 through 132 removed outlier: 3.539A pdb=" N GLY X 106 " --> pdb=" O ASP X 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.216A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 302 current: chain 'F' and resid 358 through 361 Processing sheet with id=AD7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 441 through 456 current: chain 'F' and resid 414 through 421 removed outlier: 4.220A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 305 through 309 removed outlier: 3.729A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AE4, first strand: chain 'G' and resid 154 through 162 Processing sheet with id=AE5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.711A pdb=" N LYS G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY G 441 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.734A pdb=" N VAL J 18 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL J 181 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 151 through 154 removed outlier: 3.558A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 207 " --> pdb=" O VAL J 198 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF9, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.403A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 114 through 118 removed outlier: 4.005A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 149 through 150 Processing sheet with id=AG3, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.974A pdb=" N VAL S 18 " --> pdb=" O LEU S 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AG5, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL S 181 " --> pdb=" O HIS S 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 151 through 154 removed outlier: 3.722A pdb=" N THR S 151 " --> pdb=" O ASN S 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR S 194 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU U 11 " --> pdb=" O ARG U 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP U 105 " --> pdb=" O LEU U 11 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR U 86 " --> pdb=" O THR U 102 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AH3, first strand: chain 'U' and resid 114 through 118 removed outlier: 3.551A pdb=" N PHE U 118 " --> pdb=" O VAL U 133 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL U 133 " --> pdb=" O PHE U 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER U 177 " --> pdb=" O CYS U 134 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR U 173 " --> pdb=" O ASN U 138 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 145 through 146 removed outlier: 4.238A pdb=" N LYS U 145 " --> pdb=" O THR U 197 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR U 197 " --> pdb=" O LYS U 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.514A pdb=" N ILE X 79 " --> pdb=" O CYS X 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 45 through 51 removed outlier: 4.077A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG X 50 " --> pdb=" O CYS X 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE X 37 " --> pdb=" O PHE X 95 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLY X 98 " --> pdb=" O LYS X 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS X 113 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 92 through 93 Processing sheet with id=AH8, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR X 188 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA X 148 " --> pdb=" O VAL X 196 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL X 196 " --> pdb=" O ALA X 148 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU X 150 " --> pdb=" O VAL X 194 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL X 194 " --> pdb=" O LEU X 150 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 162 through 166 removed outlier: 3.632A pdb=" N SER X 165 " --> pdb=" O ASN X 209 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.583A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 11 through 12 removed outlier: 7.162A pdb=" N VAL Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.657A pdb=" N LYS Y 45 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR Y 85 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 114 through 115 removed outlier: 4.050A pdb=" N VAL Y 132 " --> pdb=" O LEU Y 179 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Y' and resid 146 through 148 915 hydrogen bonds defined for protein. 2307 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: 6.91 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9182 1.35 - 1.47: 7883 1.47 - 1.60: 12890 1.60 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 30138 Sorted by residual: bond pdb=" O3 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 A 609 " pdb=" P PO4 A 609 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O4 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O4 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.71e+00 ... (remaining 30133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 39537 1.75 - 3.51: 1257 3.51 - 5.26: 162 5.26 - 7.02: 56 7.02 - 8.77: 11 Bond angle restraints: 41023 Sorted by residual: angle pdb=" N ASN F 156 " pdb=" CA ASN F 156 " pdb=" CB ASN F 156 " ideal model delta sigma weight residual 109.85 118.61 -8.76 1.49e+00 4.50e-01 3.45e+01 angle pdb=" N ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.54 119.51 -7.97 1.45e+00 4.76e-01 3.02e+01 angle pdb=" C ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.18 103.02 8.16 1.56e+00 4.11e-01 2.74e+01 angle pdb=" C ASN I 624 " pdb=" N ASN I 625 " pdb=" CA ASN I 625 " ideal model delta sigma weight residual 122.50 113.73 8.77 1.82e+00 3.02e-01 2.32e+01 angle pdb=" C LYS D 107 " pdb=" N ARG D 108 " pdb=" CA ARG D 108 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 ... (remaining 41018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 18533 24.42 - 48.84: 979 48.84 - 73.26: 215 73.26 - 97.67: 103 97.67 - 122.09: 31 Dihedral angle restraints: 19861 sinusoidal: 9652 harmonic: 10209 Sorted by residual: dihedral pdb=" CB CYS U 134 " pdb=" SG CYS U 134 " pdb=" SG CYS U 194 " pdb=" CB CYS U 194 " ideal model delta sinusoidal sigma weight residual -86.00 3.48 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS F 501 " pdb=" SG CYS F 501 " pdb=" SG CYS I 605 " pdb=" CB CYS I 605 " ideal model delta sinusoidal sigma weight residual 93.00 4.13 88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual -86.00 -173.74 87.74 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 19858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 5007 0.253 - 0.506: 14 0.506 - 0.759: 1 0.759 - 1.012: 0 1.012 - 1.265: 2 Chirality restraints: 5024 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN F 156 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN I 625 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C1 NAG I 701 " pdb=" ND2 ASN I 611 " pdb=" C2 NAG I 701 " pdb=" O5 NAG I 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 5021 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 156 " 0.069 2.00e-02 2.50e+03 6.67e-02 5.57e+01 pdb=" CG ASN F 156 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN F 156 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN F 156 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 625 " 0.006 2.00e-02 2.50e+03 6.42e-02 5.16e+01 pdb=" CG ASN I 625 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN I 625 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN I 625 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.039 2.00e-02 2.50e+03 3.57e-02 1.59e+01 pdb=" CG ASN A 392 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 604 " 0.038 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 584 2.67 - 3.22: 27157 3.22 - 3.78: 41957 3.78 - 4.34: 59437 4.34 - 4.90: 97531 Nonbonded interactions: 226666 Sorted by model distance: nonbonded pdb=" OD1 ASN A 386 " pdb=" OG1 THR A 388 " model vdw 2.107 3.040 nonbonded pdb=" OG SER U 63 " pdb=" OG1 THR U 74 " model vdw 2.158 3.040 nonbonded pdb=" ND2 ASN F 67 " pdb=" O ASP F 211 " model vdw 2.175 3.120 nonbonded pdb=" O TYR Y 186 " pdb=" OH TYR Y 192 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.184 3.040 ... (remaining 226661 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'F' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'G' and (resid 31 through 507 or resid 603 through 608)) } ncs_group { reference = (chain 'B' and resid 519 through 703) selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'd' selection = chain 'o' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.720 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.005 0.060 30334 Z= 0.238 Angle : 0.808 21.459 41558 Z= 0.367 Chirality : 0.057 1.265 5024 Planarity : 0.004 0.058 5042 Dihedral : 16.457 122.093 13126 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3477 helix: -1.65 (0.23), residues: 422 sheet: -0.21 (0.16), residues: 1093 loop : -1.46 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 504 TYR 0.015 0.001 TYR H 638 PHE 0.013 0.001 PHE G 53 TRP 0.032 0.001 TRP I 610 HIS 0.004 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00504 (30138) covalent geometry : angle 0.72174 (41023) SS BOND : bond 0.00472 ( 53) SS BOND : angle 2.03027 ( 106) hydrogen bonds : bond 0.21207 ( 830) hydrogen bonds : angle 7.68045 ( 2307) link_ALPHA1-2 : bond 0.00137 ( 4) link_ALPHA1-2 : angle 2.01865 ( 12) link_ALPHA1-3 : bond 0.00442 ( 12) link_ALPHA1-3 : angle 1.78244 ( 36) link_ALPHA1-6 : bond 0.00343 ( 11) link_ALPHA1-6 : angle 1.76425 ( 33) link_BETA1-4 : bond 0.00705 ( 43) link_BETA1-4 : angle 1.60871 ( 129) link_NAG-ASN : bond 0.00621 ( 73) link_NAG-ASN : angle 4.62938 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7607 (m-30) cc_final: 0.7115 (m-30) REVERT: C 28 ASN cc_start: 0.6854 (t0) cc_final: 0.6585 (t0) REVERT: C 72 ASP cc_start: 0.8449 (p0) cc_final: 0.7691 (p0) REVERT: C 145 TYR cc_start: 0.6239 (p90) cc_final: 0.6007 (p90) REVERT: D 26 ASN cc_start: 0.8538 (p0) cc_final: 0.8294 (p0) REVERT: D 70 GLU cc_start: 0.7812 (pt0) cc_final: 0.7596 (pt0) REVERT: F 213 ILE cc_start: 0.8972 (mt) cc_final: 0.8654 (tt) REVERT: K 36 TYR cc_start: 0.8729 (m-80) cc_final: 0.8489 (m-80) REVERT: S 19 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7557 (ttm170) REVERT: X 23 ASP cc_start: 0.7618 (m-30) cc_final: 0.7025 (m-30) REVERT: X 155 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7296 (mmtt) REVERT: H 620 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2234 time to fit residues: 120.8257 Evaluate side-chains 281 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 0.1980 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 478 ASN F 229 ASN G 66 HIS ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 GLN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.158305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120968 restraints weight = 44990.763| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 5.15 r_work: 0.3073 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30334 Z= 0.119 Angle : 0.659 12.827 41558 Z= 0.316 Chirality : 0.047 0.572 5024 Planarity : 0.004 0.066 5042 Dihedral : 12.124 118.900 6696 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.55 % Allowed : 6.64 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3477 helix: -0.33 (0.26), residues: 410 sheet: 0.08 (0.16), residues: 1101 loop : -1.36 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 61 TYR 0.018 0.001 TYR D 173 PHE 0.013 0.001 PHE D 118 TRP 0.014 0.001 TRP I 610 HIS 0.004 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00252 (30138) covalent geometry : angle 0.59850 (41023) SS BOND : bond 0.00472 ( 53) SS BOND : angle 1.08168 ( 106) hydrogen bonds : bond 0.04790 ( 830) hydrogen bonds : angle 5.65258 ( 2307) link_ALPHA1-2 : bond 0.00328 ( 4) link_ALPHA1-2 : angle 1.71480 ( 12) link_ALPHA1-3 : bond 0.00843 ( 12) link_ALPHA1-3 : angle 2.09605 ( 36) link_ALPHA1-6 : bond 0.00488 ( 11) link_ALPHA1-6 : angle 1.88858 ( 33) link_BETA1-4 : bond 0.00466 ( 43) link_BETA1-4 : angle 1.52303 ( 129) link_NAG-ASN : bond 0.00650 ( 73) link_NAG-ASN : angle 3.45636 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8419 (m-30) cc_final: 0.7923 (m-30) REVERT: C 74 ASP cc_start: 0.8502 (p0) cc_final: 0.8263 (p0) REVERT: C 145 TYR cc_start: 0.6614 (p90) cc_final: 0.6302 (p90) REVERT: D 3 GLN cc_start: 0.8205 (pm20) cc_final: 0.7936 (pm20) REVERT: D 26 ASN cc_start: 0.8789 (p0) cc_final: 0.8310 (p0) REVERT: D 70 GLU cc_start: 0.8161 (pt0) cc_final: 0.7892 (pt0) REVERT: F 213 ILE cc_start: 0.9146 (mt) cc_final: 0.8831 (tt) REVERT: F 274 SER cc_start: 0.9002 (p) cc_final: 0.8787 (t) REVERT: K 82 ASP cc_start: 0.6329 (m-30) cc_final: 0.5857 (m-30) REVERT: K 106 LEU cc_start: 0.6819 (mp) cc_final: 0.6574 (mp) REVERT: S 13 LYS cc_start: 0.8706 (tttm) cc_final: 0.8188 (mptt) REVERT: S 19 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7490 (ttm170) REVERT: S 28 ASN cc_start: 0.7772 (t0) cc_final: 0.7500 (t0) REVERT: S 74 ASP cc_start: 0.8653 (p0) cc_final: 0.8284 (p0) REVERT: S 98 ASP cc_start: 0.8636 (m-30) cc_final: 0.8228 (t0) REVERT: U 61 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6940 (mtm110) REVERT: U 65 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6407 (mtp-110) REVERT: U 77 ASN cc_start: 0.6045 (p0) cc_final: 0.5787 (p0) REVERT: H 620 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8089 (tm-30) outliers start: 17 outliers final: 12 residues processed: 323 average time/residue: 0.2242 time to fit residues: 110.1001 Evaluate side-chains 281 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 127 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 28 ASN U 138 ASN ** U 147 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.153847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105681 restraints weight = 45275.729| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.46 r_work: 0.3092 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 30334 Z= 0.256 Angle : 0.731 13.473 41558 Z= 0.352 Chirality : 0.050 0.471 5024 Planarity : 0.005 0.060 5042 Dihedral : 11.196 116.550 6696 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.26 % Allowed : 10.12 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3477 helix: -0.36 (0.26), residues: 419 sheet: -0.11 (0.16), residues: 1106 loop : -1.47 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 61 TYR 0.021 0.002 TYR D 49 PHE 0.018 0.002 PHE X 112 TRP 0.019 0.002 TRP J 50 HIS 0.010 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00610 (30138) covalent geometry : angle 0.67594 (41023) SS BOND : bond 0.00565 ( 53) SS BOND : angle 1.33973 ( 106) hydrogen bonds : bond 0.05199 ( 830) hydrogen bonds : angle 5.49941 ( 2307) link_ALPHA1-2 : bond 0.00249 ( 4) link_ALPHA1-2 : angle 1.95216 ( 12) link_ALPHA1-3 : bond 0.00928 ( 12) link_ALPHA1-3 : angle 2.08090 ( 36) link_ALPHA1-6 : bond 0.00556 ( 11) link_ALPHA1-6 : angle 2.03071 ( 33) link_BETA1-4 : bond 0.00523 ( 43) link_BETA1-4 : angle 1.52141 ( 129) link_NAG-ASN : bond 0.00535 ( 73) link_NAG-ASN : angle 3.46015 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8615 (m-30) cc_final: 0.8197 (m-30) REVERT: C 145 TYR cc_start: 0.6774 (p90) cc_final: 0.6408 (p90) REVERT: D 3 GLN cc_start: 0.8371 (pm20) cc_final: 0.8019 (pm20) REVERT: D 26 ASN cc_start: 0.9014 (p0) cc_final: 0.8707 (p0) REVERT: D 70 GLU cc_start: 0.8282 (pt0) cc_final: 0.7875 (pt0) REVERT: D 81 GLU cc_start: 0.7987 (mp0) cc_final: 0.7619 (mp0) REVERT: F 213 ILE cc_start: 0.9154 (mt) cc_final: 0.8844 (tt) REVERT: G 205 CYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7060 (m) REVERT: G 207 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8272 (pptt) REVERT: K 82 ASP cc_start: 0.6386 (m-30) cc_final: 0.5956 (m-30) REVERT: K 106 LEU cc_start: 0.7110 (mp) cc_final: 0.6847 (mp) REVERT: S 19 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7614 (ttm170) REVERT: S 98 ASP cc_start: 0.8787 (m-30) cc_final: 0.8306 (t0) REVERT: U 61 ARG cc_start: 0.7238 (mtm110) cc_final: 0.6867 (mtm110) REVERT: U 77 ASN cc_start: 0.6000 (p0) cc_final: 0.5721 (p0) REVERT: Y 166 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6318 (mm-40) REVERT: H 620 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8277 (tm-30) outliers start: 39 outliers final: 25 residues processed: 299 average time/residue: 0.2185 time to fit residues: 99.3396 Evaluate side-chains 290 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 260 optimal weight: 20.0000 chunk 321 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 278 optimal weight: 20.0000 chunk 124 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN F 114 GLN G 66 HIS S 204 ASN ** U 147 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.155038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107362 restraints weight = 45011.281| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.46 r_work: 0.3100 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30334 Z= 0.190 Angle : 0.668 13.374 41558 Z= 0.321 Chirality : 0.047 0.306 5024 Planarity : 0.004 0.069 5042 Dihedral : 10.300 115.647 6696 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.26 % Allowed : 12.79 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3477 helix: -0.18 (0.26), residues: 419 sheet: -0.13 (0.16), residues: 1096 loop : -1.45 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 61 TYR 0.018 0.001 TYR X 157 PHE 0.018 0.001 PHE G 53 TRP 0.016 0.002 TRP J 50 HIS 0.005 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00446 (30138) covalent geometry : angle 0.61525 (41023) SS BOND : bond 0.00481 ( 53) SS BOND : angle 1.28394 ( 106) hydrogen bonds : bond 0.04503 ( 830) hydrogen bonds : angle 5.19656 ( 2307) link_ALPHA1-2 : bond 0.00170 ( 4) link_ALPHA1-2 : angle 1.82056 ( 12) link_ALPHA1-3 : bond 0.01039 ( 12) link_ALPHA1-3 : angle 2.15570 ( 36) link_ALPHA1-6 : bond 0.00669 ( 11) link_ALPHA1-6 : angle 1.90791 ( 33) link_BETA1-4 : bond 0.00494 ( 43) link_BETA1-4 : angle 1.39736 ( 129) link_NAG-ASN : bond 0.00471 ( 73) link_NAG-ASN : angle 3.20354 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9169 (mt) REVERT: A 107 ASP cc_start: 0.8624 (m-30) cc_final: 0.8198 (m-30) REVERT: C 145 TYR cc_start: 0.6791 (p90) cc_final: 0.6477 (p90) REVERT: D 3 GLN cc_start: 0.8349 (pm20) cc_final: 0.7996 (pm20) REVERT: D 26 ASN cc_start: 0.9000 (p0) cc_final: 0.8646 (p0) REVERT: D 70 GLU cc_start: 0.8286 (pt0) cc_final: 0.7889 (pt0) REVERT: D 81 GLU cc_start: 0.8026 (mp0) cc_final: 0.7680 (mp0) REVERT: F 213 ILE cc_start: 0.9136 (mt) cc_final: 0.8807 (tt) REVERT: J 87 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8265 (t) REVERT: K 82 ASP cc_start: 0.6728 (m-30) cc_final: 0.6262 (m-30) REVERT: S 13 LYS cc_start: 0.8742 (tttm) cc_final: 0.8246 (mptt) REVERT: S 19 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7588 (ttm170) REVERT: S 28 ASN cc_start: 0.7794 (t0) cc_final: 0.7308 (t0) REVERT: S 31 ASP cc_start: 0.8045 (m-30) cc_final: 0.7572 (m-30) REVERT: S 82 LEU cc_start: 0.8385 (mt) cc_final: 0.8164 (mt) REVERT: S 98 ASP cc_start: 0.8797 (m-30) cc_final: 0.8312 (t0) REVERT: U 61 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6859 (mtm110) REVERT: U 77 ASN cc_start: 0.5961 (p0) cc_final: 0.5652 (p0) REVERT: X 157 TYR cc_start: 0.5457 (p90) cc_final: 0.5007 (p90) REVERT: I 634 GLU cc_start: 0.8885 (pp20) cc_final: 0.8670 (pp20) REVERT: H 620 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 39 outliers final: 27 residues processed: 302 average time/residue: 0.2105 time to fit residues: 97.6926 Evaluate side-chains 291 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 262 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 320 optimal weight: 0.4980 chunk 234 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 271 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN G 66 HIS U 138 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121236 restraints weight = 44999.395| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.29 r_work: 0.3015 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30334 Z= 0.138 Angle : 0.628 13.017 41558 Z= 0.302 Chirality : 0.046 0.310 5024 Planarity : 0.004 0.058 5042 Dihedral : 9.688 114.874 6696 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.61 % Allowed : 13.37 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3477 helix: 0.03 (0.27), residues: 419 sheet: 0.03 (0.16), residues: 1080 loop : -1.40 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 61 TYR 0.014 0.001 TYR X 157 PHE 0.013 0.001 PHE G 53 TRP 0.014 0.001 TRP C 50 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00316 (30138) covalent geometry : angle 0.57663 (41023) SS BOND : bond 0.00437 ( 53) SS BOND : angle 1.10873 ( 106) hydrogen bonds : bond 0.04054 ( 830) hydrogen bonds : angle 4.95880 ( 2307) link_ALPHA1-2 : bond 0.00183 ( 4) link_ALPHA1-2 : angle 1.75717 ( 12) link_ALPHA1-3 : bond 0.01079 ( 12) link_ALPHA1-3 : angle 2.13478 ( 36) link_ALPHA1-6 : bond 0.00774 ( 11) link_ALPHA1-6 : angle 1.80595 ( 33) link_BETA1-4 : bond 0.00465 ( 43) link_BETA1-4 : angle 1.33268 ( 129) link_NAG-ASN : bond 0.00426 ( 73) link_NAG-ASN : angle 3.07555 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9115 (mt) REVERT: A 107 ASP cc_start: 0.8483 (m-30) cc_final: 0.8034 (m-30) REVERT: C 87 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (t) REVERT: C 95 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8829 (pt0) REVERT: C 145 TYR cc_start: 0.6769 (p90) cc_final: 0.6513 (p90) REVERT: C 178 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5958 (pp) REVERT: D 26 ASN cc_start: 0.8976 (p0) cc_final: 0.8421 (p0) REVERT: D 70 GLU cc_start: 0.8181 (pt0) cc_final: 0.7854 (pt0) REVERT: D 81 GLU cc_start: 0.8036 (mp0) cc_final: 0.7689 (mp0) REVERT: F 213 ILE cc_start: 0.9083 (mt) cc_final: 0.8746 (tt) REVERT: K 82 ASP cc_start: 0.6703 (m-30) cc_final: 0.6241 (m-30) REVERT: S 13 LYS cc_start: 0.8736 (tttm) cc_final: 0.8251 (mptt) REVERT: S 19 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7553 (ttm170) REVERT: S 28 ASN cc_start: 0.7750 (t0) cc_final: 0.7260 (t0) REVERT: S 31 ASP cc_start: 0.7941 (m-30) cc_final: 0.7428 (m-30) REVERT: S 82 LEU cc_start: 0.8307 (mt) cc_final: 0.8100 (mt) REVERT: S 98 ASP cc_start: 0.8676 (m-30) cc_final: 0.8249 (t0) REVERT: X 119 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6127 (pp) REVERT: Y 166 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6420 (mm-40) REVERT: H 620 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8292 (tm-30) outliers start: 50 outliers final: 29 residues processed: 310 average time/residue: 0.1985 time to fit residues: 96.0711 Evaluate side-chains 301 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 205 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN S 204 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121846 restraints weight = 45001.510| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 4.18 r_work: 0.3011 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30334 Z= 0.160 Angle : 0.638 12.781 41558 Z= 0.307 Chirality : 0.046 0.310 5024 Planarity : 0.004 0.056 5042 Dihedral : 9.434 113.593 6696 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.87 % Allowed : 14.28 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3477 helix: 0.09 (0.27), residues: 419 sheet: 0.03 (0.16), residues: 1098 loop : -1.42 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 61 TYR 0.013 0.001 TYR D 49 PHE 0.013 0.001 PHE X 112 TRP 0.014 0.001 TRP J 50 HIS 0.004 0.001 HIS G 375 Details of bonding type rmsd covalent geometry : bond 0.00374 (30138) covalent geometry : angle 0.58745 (41023) SS BOND : bond 0.00445 ( 53) SS BOND : angle 1.26484 ( 106) hydrogen bonds : bond 0.04103 ( 830) hydrogen bonds : angle 4.89395 ( 2307) link_ALPHA1-2 : bond 0.00147 ( 4) link_ALPHA1-2 : angle 1.79294 ( 12) link_ALPHA1-3 : bond 0.01065 ( 12) link_ALPHA1-3 : angle 2.17019 ( 36) link_ALPHA1-6 : bond 0.00779 ( 11) link_ALPHA1-6 : angle 1.84122 ( 33) link_BETA1-4 : bond 0.00485 ( 43) link_BETA1-4 : angle 1.33309 ( 129) link_NAG-ASN : bond 0.00493 ( 73) link_NAG-ASN : angle 3.03603 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9128 (mt) REVERT: A 107 ASP cc_start: 0.8505 (m-30) cc_final: 0.8083 (m-30) REVERT: A 166 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.6944 (mtm180) REVERT: C 87 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7815 (t) REVERT: C 95 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8822 (pt0) REVERT: C 178 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5833 (pp) REVERT: D 26 ASN cc_start: 0.8875 (p0) cc_final: 0.8505 (p0) REVERT: D 70 GLU cc_start: 0.8144 (pt0) cc_final: 0.7805 (pt0) REVERT: D 81 GLU cc_start: 0.8020 (mp0) cc_final: 0.7671 (mp0) REVERT: F 213 ILE cc_start: 0.9062 (mt) cc_final: 0.8716 (tt) REVERT: F 426 MET cc_start: 0.7458 (tpp) cc_final: 0.7000 (tpt) REVERT: J 87 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8229 (t) REVERT: K 82 ASP cc_start: 0.6663 (m-30) cc_final: 0.6203 (m-30) REVERT: S 13 LYS cc_start: 0.8717 (tttm) cc_final: 0.8246 (mptt) REVERT: S 19 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7443 (ttm170) REVERT: S 28 ASN cc_start: 0.7730 (t0) cc_final: 0.7106 (t0) REVERT: S 31 ASP cc_start: 0.7952 (m-30) cc_final: 0.7375 (m-30) REVERT: S 82 LEU cc_start: 0.8348 (mt) cc_final: 0.8136 (mt) REVERT: S 98 ASP cc_start: 0.8671 (m-30) cc_final: 0.8230 (t0) REVERT: X 119 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6082 (pp) REVERT: X 157 TYR cc_start: 0.4137 (p90) cc_final: 0.3898 (p90) REVERT: Y 166 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6426 (mm-40) REVERT: H 545 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8553 (tt) REVERT: H 620 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8295 (tm-30) outliers start: 58 outliers final: 42 residues processed: 315 average time/residue: 0.1956 time to fit residues: 95.7095 Evaluate side-chains 318 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain H residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 309 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 332 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 478 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122193 restraints weight = 44979.146| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.20 r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30334 Z= 0.139 Angle : 0.622 12.606 41558 Z= 0.299 Chirality : 0.046 0.310 5024 Planarity : 0.004 0.055 5042 Dihedral : 9.179 112.927 6696 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.97 % Allowed : 15.11 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3477 helix: 0.12 (0.27), residues: 425 sheet: 0.06 (0.16), residues: 1079 loop : -1.38 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 61 TYR 0.031 0.001 TYR C 145 PHE 0.013 0.001 PHE X 112 TRP 0.014 0.001 TRP J 50 HIS 0.006 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00321 (30138) covalent geometry : angle 0.57325 (41023) SS BOND : bond 0.00450 ( 53) SS BOND : angle 1.11481 ( 106) hydrogen bonds : bond 0.03912 ( 830) hydrogen bonds : angle 4.80893 ( 2307) link_ALPHA1-2 : bond 0.00159 ( 4) link_ALPHA1-2 : angle 1.75170 ( 12) link_ALPHA1-3 : bond 0.01092 ( 12) link_ALPHA1-3 : angle 2.14273 ( 36) link_ALPHA1-6 : bond 0.00817 ( 11) link_ALPHA1-6 : angle 1.81580 ( 33) link_BETA1-4 : bond 0.00473 ( 43) link_BETA1-4 : angle 1.30811 ( 129) link_NAG-ASN : bond 0.00440 ( 73) link_NAG-ASN : angle 2.98815 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9094 (mt) REVERT: A 107 ASP cc_start: 0.8494 (m-30) cc_final: 0.8071 (m-30) REVERT: A 166 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.6857 (mtm180) REVERT: C 87 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7776 (t) REVERT: C 95 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8818 (pt0) REVERT: D 26 ASN cc_start: 0.8870 (p0) cc_final: 0.8483 (p0) REVERT: D 70 GLU cc_start: 0.8199 (pt0) cc_final: 0.7898 (pt0) REVERT: D 81 GLU cc_start: 0.8014 (mp0) cc_final: 0.7677 (mp0) REVERT: D 146 VAL cc_start: 0.5738 (OUTLIER) cc_final: 0.5481 (p) REVERT: F 213 ILE cc_start: 0.9131 (mt) cc_final: 0.8792 (tt) REVERT: F 426 MET cc_start: 0.7437 (tpp) cc_final: 0.7035 (tpt) REVERT: G 205 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6831 (m) REVERT: J 87 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8256 (t) REVERT: K 82 ASP cc_start: 0.6680 (m-30) cc_final: 0.6231 (m-30) REVERT: S 13 LYS cc_start: 0.8703 (tttm) cc_final: 0.8234 (mptt) REVERT: S 19 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7415 (ttm170) REVERT: S 82 LEU cc_start: 0.8338 (mt) cc_final: 0.8001 (mt) REVERT: S 98 ASP cc_start: 0.8629 (m-30) cc_final: 0.8195 (t0) REVERT: X 119 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6076 (pp) REVERT: Y 166 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6421 (mm-40) REVERT: H 545 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8572 (tt) REVERT: H 620 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8289 (tm-30) outliers start: 61 outliers final: 43 residues processed: 313 average time/residue: 0.2089 time to fit residues: 100.7401 Evaluate side-chains 316 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain H residue 545 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 314 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 274 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 280 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123274 restraints weight = 45113.360| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.20 r_work: 0.3045 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30334 Z= 0.115 Angle : 0.603 12.532 41558 Z= 0.290 Chirality : 0.046 0.310 5024 Planarity : 0.004 0.055 5042 Dihedral : 8.804 111.991 6696 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.93 % Allowed : 15.47 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3477 helix: 0.43 (0.27), residues: 411 sheet: 0.15 (0.16), residues: 1094 loop : -1.35 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 61 TYR 0.013 0.001 TYR X 157 PHE 0.011 0.001 PHE X 112 TRP 0.013 0.001 TRP C 50 HIS 0.007 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00258 (30138) covalent geometry : angle 0.55590 (41023) SS BOND : bond 0.00400 ( 53) SS BOND : angle 0.94903 ( 106) hydrogen bonds : bond 0.03599 ( 830) hydrogen bonds : angle 4.66214 ( 2307) link_ALPHA1-2 : bond 0.00214 ( 4) link_ALPHA1-2 : angle 1.66953 ( 12) link_ALPHA1-3 : bond 0.01106 ( 12) link_ALPHA1-3 : angle 2.07944 ( 36) link_ALPHA1-6 : bond 0.00871 ( 11) link_ALPHA1-6 : angle 1.76485 ( 33) link_BETA1-4 : bond 0.00460 ( 43) link_BETA1-4 : angle 1.26439 ( 129) link_NAG-ASN : bond 0.00472 ( 73) link_NAG-ASN : angle 2.88717 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9075 (mt) REVERT: A 107 ASP cc_start: 0.8472 (m-30) cc_final: 0.8020 (m-30) REVERT: A 166 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7340 (mtm110) REVERT: C 87 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7759 (t) REVERT: C 95 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8948 (pt0) REVERT: C 178 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5702 (pp) REVERT: D 26 ASN cc_start: 0.8801 (p0) cc_final: 0.8410 (p0) REVERT: D 81 GLU cc_start: 0.8039 (mp0) cc_final: 0.7684 (mp0) REVERT: D 146 VAL cc_start: 0.5739 (OUTLIER) cc_final: 0.5481 (p) REVERT: F 213 ILE cc_start: 0.9106 (mt) cc_final: 0.8779 (tt) REVERT: F 426 MET cc_start: 0.7398 (tpp) cc_final: 0.7032 (tpt) REVERT: G 207 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8185 (pptt) REVERT: J 87 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8254 (t) REVERT: J 201 LYS cc_start: 0.6885 (tptt) cc_final: 0.6666 (tppt) REVERT: K 82 ASP cc_start: 0.6699 (m-30) cc_final: 0.6257 (m-30) REVERT: S 13 LYS cc_start: 0.8699 (tttm) cc_final: 0.8243 (mptt) REVERT: S 19 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7395 (ttm170) REVERT: S 98 ASP cc_start: 0.8632 (m-30) cc_final: 0.8203 (t0) REVERT: U 76 ASN cc_start: 0.7871 (m-40) cc_final: 0.6821 (m110) REVERT: X 119 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.6077 (pp) REVERT: Y 166 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6608 (mm-40) REVERT: H 620 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8287 (tm-30) outliers start: 60 outliers final: 40 residues processed: 320 average time/residue: 0.1951 time to fit residues: 96.7890 Evaluate side-chains 310 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 225 optimal weight: 4.9990 chunk 342 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 77 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121103 restraints weight = 44890.606| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.44 r_work: 0.3050 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30334 Z= 0.120 Angle : 0.608 12.304 41558 Z= 0.292 Chirality : 0.046 0.311 5024 Planarity : 0.004 0.055 5042 Dihedral : 8.644 111.248 6696 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.87 % Allowed : 15.73 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.92 (0.14), residues: 3477 helix: 0.48 (0.27), residues: 411 sheet: 0.13 (0.16), residues: 1108 loop : -1.32 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 61 TYR 0.013 0.001 TYR X 157 PHE 0.011 0.001 PHE X 112 TRP 0.013 0.001 TRP C 50 HIS 0.006 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00274 (30138) covalent geometry : angle 0.55934 (41023) SS BOND : bond 0.00402 ( 53) SS BOND : angle 1.33739 ( 106) hydrogen bonds : bond 0.03584 ( 830) hydrogen bonds : angle 4.62479 ( 2307) link_ALPHA1-2 : bond 0.00193 ( 4) link_ALPHA1-2 : angle 1.67199 ( 12) link_ALPHA1-3 : bond 0.01075 ( 12) link_ALPHA1-3 : angle 2.05659 ( 36) link_ALPHA1-6 : bond 0.00893 ( 11) link_ALPHA1-6 : angle 1.75454 ( 33) link_BETA1-4 : bond 0.00468 ( 43) link_BETA1-4 : angle 1.25194 ( 129) link_NAG-ASN : bond 0.00508 ( 73) link_NAG-ASN : angle 2.88763 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 107 ASP cc_start: 0.8420 (m-30) cc_final: 0.7956 (m-30) REVERT: A 166 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7246 (mtm110) REVERT: A 440 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8167 (ptm160) REVERT: C 87 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7758 (t) REVERT: C 95 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8961 (pt0) REVERT: C 178 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5651 (pp) REVERT: D 26 ASN cc_start: 0.8807 (p0) cc_final: 0.8416 (p0) REVERT: D 81 GLU cc_start: 0.8019 (mp0) cc_final: 0.7668 (mp0) REVERT: D 146 VAL cc_start: 0.5726 (OUTLIER) cc_final: 0.5459 (p) REVERT: F 213 ILE cc_start: 0.9147 (mt) cc_final: 0.8815 (tt) REVERT: F 426 MET cc_start: 0.7405 (tpp) cc_final: 0.7039 (tpt) REVERT: G 207 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8203 (pptt) REVERT: J 87 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8210 (t) REVERT: J 201 LYS cc_start: 0.6979 (tptt) cc_final: 0.6735 (tppt) REVERT: S 19 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7405 (ttm170) REVERT: S 28 ASN cc_start: 0.7622 (t0) cc_final: 0.7377 (t0) REVERT: S 98 ASP cc_start: 0.8588 (m-30) cc_final: 0.8193 (t0) REVERT: U 61 ARG cc_start: 0.6505 (mtm110) cc_final: 0.6216 (mtm110) REVERT: X 119 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6048 (pp) REVERT: Y 166 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6561 (mm-40) REVERT: H 620 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8255 (tm-30) outliers start: 58 outliers final: 45 residues processed: 305 average time/residue: 0.2060 time to fit residues: 96.6292 Evaluate side-chains 321 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 166 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 17 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 198 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN S 46 GLN S 62 GLN U 76 ASN ** U 147 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.157212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123229 restraints weight = 44709.502| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.07 r_work: 0.3048 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30334 Z= 0.127 Angle : 0.611 12.248 41558 Z= 0.294 Chirality : 0.046 0.312 5024 Planarity : 0.004 0.056 5042 Dihedral : 8.478 109.977 6696 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.71 % Allowed : 16.05 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3477 helix: 0.49 (0.27), residues: 412 sheet: 0.13 (0.16), residues: 1108 loop : -1.32 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 61 TYR 0.012 0.001 TYR X 157 PHE 0.012 0.001 PHE G 53 TRP 0.013 0.001 TRP C 50 HIS 0.006 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00291 (30138) covalent geometry : angle 0.56407 (41023) SS BOND : bond 0.00407 ( 53) SS BOND : angle 1.28396 ( 106) hydrogen bonds : bond 0.03627 ( 830) hydrogen bonds : angle 4.59050 ( 2307) link_ALPHA1-2 : bond 0.00163 ( 4) link_ALPHA1-2 : angle 1.67484 ( 12) link_ALPHA1-3 : bond 0.01048 ( 12) link_ALPHA1-3 : angle 2.02063 ( 36) link_ALPHA1-6 : bond 0.00916 ( 11) link_ALPHA1-6 : angle 1.71053 ( 33) link_BETA1-4 : bond 0.00479 ( 43) link_BETA1-4 : angle 1.24427 ( 129) link_NAG-ASN : bond 0.00453 ( 73) link_NAG-ASN : angle 2.87664 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9125 (mt) REVERT: A 107 ASP cc_start: 0.8471 (m-30) cc_final: 0.8027 (m-30) REVERT: A 166 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7298 (mtm110) REVERT: A 440 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.8177 (ptm160) REVERT: C 87 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7779 (t) REVERT: C 95 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (pt0) REVERT: C 178 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5609 (pp) REVERT: D 26 ASN cc_start: 0.8812 (p0) cc_final: 0.8427 (p0) REVERT: D 146 VAL cc_start: 0.5724 (OUTLIER) cc_final: 0.5463 (p) REVERT: F 426 MET cc_start: 0.7407 (tpp) cc_final: 0.7025 (tpt) REVERT: G 207 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8187 (pptt) REVERT: J 87 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8197 (t) REVERT: K 82 ASP cc_start: 0.6577 (m-30) cc_final: 0.6098 (m-30) REVERT: S 19 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7346 (ttm170) REVERT: S 98 ASP cc_start: 0.8589 (m-30) cc_final: 0.8177 (t0) REVERT: H 620 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8289 (tm-30) outliers start: 53 outliers final: 44 residues processed: 310 average time/residue: 0.2136 time to fit residues: 101.0951 Evaluate side-chains 316 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 251 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 0.0070 chunk 299 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 340 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN F 99 ASN S 204 ASN U 76 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 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 = 0.3973 r_free = 0.3973 target = 0.157637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123707 restraints weight = 45022.783| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.12 r_work: 0.3051 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30334 Z= 0.118 Angle : 0.600 12.181 41558 Z= 0.289 Chirality : 0.045 0.310 5024 Planarity : 0.004 0.056 5042 Dihedral : 8.300 109.252 6696 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.74 % Allowed : 15.92 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3477 helix: 0.56 (0.27), residues: 411 sheet: 0.15 (0.16), residues: 1106 loop : -1.29 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 40 TYR 0.012 0.001 TYR U 91 PHE 0.011 0.001 PHE G 53 TRP 0.013 0.001 TRP C 50 HIS 0.005 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00268 (30138) covalent geometry : angle 0.55327 (41023) SS BOND : bond 0.00388 ( 53) SS BOND : angle 1.18854 ( 106) hydrogen bonds : bond 0.03532 ( 830) hydrogen bonds : angle 4.53881 ( 2307) link_ALPHA1-2 : bond 0.00199 ( 4) link_ALPHA1-2 : angle 1.64879 ( 12) link_ALPHA1-3 : bond 0.01010 ( 12) link_ALPHA1-3 : angle 1.97318 ( 36) link_ALPHA1-6 : bond 0.00957 ( 11) link_ALPHA1-6 : angle 1.67896 ( 33) link_BETA1-4 : bond 0.00474 ( 43) link_BETA1-4 : angle 1.22758 ( 129) link_NAG-ASN : bond 0.00451 ( 73) link_NAG-ASN : angle 2.85316 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6714.19 seconds wall clock time: 116 minutes 14.25 seconds (6974.25 seconds total)