Starting phenix.real_space_refine on Sun Jul 5 18:03:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n28_24128/07_2026/7n28_24128.map" } resolution = 4.2 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= 0.001 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 143 5.16 5 C 18487 2.51 5 N 4838 2.21 5 O 5990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29461 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: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 209} Chain breaks: 1 Chain: "Y" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "M" 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: "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: "N" 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 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 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 chiralities: 2 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "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 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 1 Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 150 Unusual residues: {'NAG': 10, 'PO4': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 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 chiralities: 1 Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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 chiralities: 1 Chain: "X" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" 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 chiralities: 3 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 chiralities: 4 Chain: "N" 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 chiralities: 3 Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 29461 At special positions: 0 Unit cell: (184.62, 178.5, 181.56, 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 143 16.00 P 3 15.00 O 5990 8.00 N 4838 7.00 C 18487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 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=2.03 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=2.04 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=2.04 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 M 605 " distance=2.03 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 N 605 " distance=2.04 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=2.03 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=2.03 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 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 M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 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=1, symmetry=0 Links applied ALPHA1-2 " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA L 3 " - " MAN L 4 " " MAN L 7 " - " MAN L 8 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA k 3 " - " MAN k 6 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA L 3 " - " MAN L 7 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA k 3 " - " MAN k 4 " " MAN k 4 " - " MAN k 5 " " BMA m 3 " - " MAN m 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 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 448 " " NAG F 608 " - " ASN F 149 " " NAG F 609 " - " ASN F 241 " " NAG F 610 " - " ASN F 355 " " NAG F 611 " - " ASN F 405 " " NAG F 612 " - " 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 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 197 " " NAG K 301 " - " ASN K 72 " " NAG L 1 " - " ASN A 262 " " NAG M 701 " - " ASN M 611 " " NAG M 702 " - " ASN M 637 " " NAG M 703 " - " ASN M 616 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG N 703 " - " ASN N 625 " " 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 M 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 88 " " NAG i 1 " - " ASN F 334 " " NAG j 1 " - " ASN F 289 " " NAG k 1 " - " ASN F 160 " " NAG l 1 " - " ASN G 156 " " NAG m 1 " - " ASN G 262 " " NAG n 1 " - " ASN G 276 " " NAG o 1 " - " ASN G 295 " " NAG p 1 " - " ASN G 386 " " NAG q 1 " - " ASN G 448 " " NAG r 1 " - " ASN G 88 " " NAG s 1 " - " ASN G 334 " " NAG t 1 " - " ASN G 241 " " NAG u 1 " - " ASN G 289 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 78 sheets defined 13.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.733A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.677A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.200A pdb=" N GLU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.919A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.598A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.536A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.319A 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 335 through 351 removed outlier: 4.109A pdb=" N GLU F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.979A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.582A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.914A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.943A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 4.109A 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 121 through 126 removed outlier: 3.654A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.707A 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 183 through 189 removed outlier: 3.692A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 158 No H-bonds generated for 'chain 'S' and resid 156 through 158' Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'U' and resid 122 through 127 removed outlier: 3.725A pdb=" N SER U 127 " --> pdb=" O GLU U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 188 removed outlier: 3.787A pdb=" N GLU U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 61 through 65 removed outlier: 3.651A pdb=" N THR X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 removed outlier: 4.080A pdb=" N THR X 91 " --> pdb=" O ALA X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 170 No H-bonds generated for 'chain 'X' and resid 168 through 170' Processing helix chain 'Y' and resid 121 through 127 Processing helix chain 'M' and resid 529 through 534 removed outlier: 3.920A pdb=" N SER M 534 " --> pdb=" O MET M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 537 No H-bonds generated for 'chain 'M' and resid 535 through 537' Processing helix chain 'M' and resid 547 through 551 removed outlier: 3.517A pdb=" N GLN M 550 " --> pdb=" O GLY M 547 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 597 removed outlier: 4.202A pdb=" N LEU M 576 " --> pdb=" O GLY M 572 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 589 " --> pdb=" O ARG M 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE M 592 " --> pdb=" O GLU M 588 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY M 597 " --> pdb=" O LEU M 593 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 624 Processing helix chain 'M' and resid 627 through 635 removed outlier: 3.882A pdb=" N GLU M 632 " --> pdb=" O TRP M 628 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG M 633 " --> pdb=" O ILE M 629 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU M 634 " --> pdb=" O GLU M 630 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE M 635 " --> pdb=" O TRP M 631 " (cutoff:3.500A) Processing helix chain 'M' and resid 638 through 659 removed outlier: 4.230A pdb=" N ASP M 644 " --> pdb=" O SER M 640 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR M 647 " --> pdb=" O TYR M 643 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP M 654 " --> pdb=" O GLN M 650 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN M 656 " --> pdb=" O GLN M 652 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP M 659 " --> pdb=" O ILE M 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.587A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.088A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 removed outlier: 3.507A pdb=" N THR B 569 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 4.470A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.672A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.906A pdb=" N THR B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 531 through 535 removed outlier: 4.081A pdb=" N ASN N 535 " --> pdb=" O ALA N 532 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 543 removed outlier: 4.295A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN N 543 " --> pdb=" O VAL N 539 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 551 removed outlier: 3.724A pdb=" N GLN N 550 " --> pdb=" O GLY N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 569 through 596 removed outlier: 3.514A pdb=" N LYS N 574 " --> pdb=" O VAL N 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL N 589 " --> pdb=" O ARG N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 624 removed outlier: 3.552A pdb=" N ASN N 624 " --> pdb=" O GLU N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.947A pdb=" N ARG N 633 " --> pdb=" O ILE N 629 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU N 634 " --> pdb=" O GLU N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 641 Processing helix chain 'N' and resid 642 through 659 removed outlier: 3.503A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP N 659 " --> pdb=" O ILE N 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.587A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.737A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.629A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.770A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.502A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.741A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.697A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.936A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.187A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.637A pdb=" N LEU C 5 " --> pdb=" O GLU C 23 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 24 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.725A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 89 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.871A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.871A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.804A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 211 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.512A pdb=" N GLU D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 72 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.822A pdb=" N TYR D 49 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 115 removed outlier: 4.000A pdb=" N CYS D 134 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D 177 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 144 through 148 removed outlier: 4.192A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 209 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.527A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.229A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR F 217 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS F 249 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.715A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 132 removed outlier: 3.793A pdb=" N PHE F 176 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.561A pdb=" N GLN F 170 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 181 through 182 Processing sheet with id=AD1, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.684A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ASN F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N ILE F 294 " --> pdb=" O ASN F 444 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N ASN F 448 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 304 through 308 removed outlier: 3.511A pdb=" N THR F 305 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AD4, first strand: chain 'F' and resid 393 through 395 removed outlier: 3.628A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 374 through 378 removed outlier: 4.083A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.543A pdb=" N ALA G 497 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.561A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.886A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AE1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.828A pdb=" N TYR G 435 " --> pdb=" O LYS G 202 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ASN G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ILE G 294 " --> pdb=" O ASN G 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN G 448 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LYS G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ASN G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ILE G 294 " --> pdb=" O ASN G 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN G 448 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LYS G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU G 293 " --> pdb=" O ASN G 334 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.420A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 393 through 395 removed outlier: 3.838A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.511A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 89 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.852A pdb=" N VAL J 20 " --> pdb=" O MET J 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 120 through 123 removed outlier: 3.512A pdb=" N SER J 120 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS J 143 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 120 through 123 removed outlier: 3.512A pdb=" N SER J 120 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS J 143 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AF3, first strand: chain 'J' and resid 150 through 154 removed outlier: 4.062A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 199 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR J 194 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS J 196 " --> pdb=" O LYS J 209 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS J 209 " --> pdb=" O CYS J 196 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL J 198 " --> pdb=" O VAL J 207 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL J 207 " --> pdb=" O VAL J 198 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.731A pdb=" N GLN K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.947A pdb=" N LEU K 11 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.587A pdb=" N LYS K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.550A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 177 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR K 178 " --> pdb=" O GLN K 160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 144 through 145 Processing sheet with id=AF9, first strand: chain 'K' and resid 148 through 149 removed outlier: 4.060A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AG2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.695A pdb=" N THR S 110 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 109 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL S 89 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.695A pdb=" N THR S 110 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 109 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 120 through 123 removed outlier: 3.944A pdb=" N SER S 120 " --> pdb=" O LYS S 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU S 141 " --> pdb=" O PHE S 122 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS S 143 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU S 178 " --> pdb=" O LYS S 143 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR S 145 " --> pdb=" O TYR S 176 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 150 through 154 removed outlier: 3.524A pdb=" N ASN S 199 " --> pdb=" O THR S 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR S 194 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL S 198 " --> pdb=" O VAL S 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL S 207 " --> pdb=" O VAL S 198 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 163 through 165 Processing sheet with id=AG7, first strand: chain 'U' and resid 53 through 54 removed outlier: 5.232A pdb=" N LEU U 46 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN U 37 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 114 through 117 removed outlier: 3.747A pdb=" N ASN U 137 " --> pdb=" O SER U 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA U 130 " --> pdb=" O LEU U 181 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR U 173 " --> pdb=" O ASN U 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 144 through 146 removed outlier: 3.636A pdb=" N THR U 197 " --> pdb=" O LYS U 145 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 149 through 150 removed outlier: 3.832A pdb=" N ALA U 193 " --> pdb=" O LYS U 149 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 4 through 5 removed outlier: 3.506A pdb=" N ILE X 79 " --> pdb=" O CYS X 22 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL X 80 " --> pdb=" O SER X 71 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.832A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY X 49 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP X 36 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS X 34 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER X 114 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.832A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY X 49 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP X 36 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS X 34 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU X 119 " --> pdb=" O TYR X 94 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 132 through 135 removed outlier: 3.808A pdb=" N LYS X 155 " --> pdb=" O LEU X 190 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU X 190 " --> pdb=" O LYS X 155 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR X 188 " --> pdb=" O TYR X 157 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL X 181 " --> pdb=" O SER X 189 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 163 through 166 removed outlier: 4.021A pdb=" N THR X 163 " --> pdb=" O ASN X 211 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.859A pdb=" N VAL Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'Y' and resid 20 through 24 removed outlier: 3.727A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AI1, first strand: chain 'Y' and resid 45 through 46 removed outlier: 4.025A pdb=" N THR Y 85 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 48 through 49 Processing sheet with id=AI3, first strand: chain 'Y' and resid 117 through 118 removed outlier: 3.907A pdb=" N VAL Y 133 " --> pdb=" O PHE Y 118 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 129 through 130 Processing sheet with id=AI5, first strand: chain 'Y' and resid 136 through 139 removed outlier: 5.583A pdb=" N TYR Y 173 " --> pdb=" O ASN Y 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Y' and resid 147 through 148 708 hydrogen bonds defined for protein. 1821 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: 6.36 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9090 1.34 - 1.46: 7631 1.46 - 1.59: 13203 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 30104 Sorted by residual: bond pdb=" C1 NAG A 607 " pdb=" O5 NAG A 607 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 NAG N 703 " pdb=" O5 NAG N 703 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.09e+00 ... (remaining 30099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39690 1.94 - 3.88: 1058 3.88 - 5.82: 167 5.82 - 7.77: 48 7.77 - 9.71: 7 Bond angle restraints: 40970 Sorted by residual: angle pdb=" C ASN A 448 " pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " ideal model delta sigma weight residual 111.70 121.41 -9.71 1.31e+00 5.83e-01 5.49e+01 angle pdb=" C ASN N 625 " pdb=" CA ASN N 625 " pdb=" CB ASN N 625 " ideal model delta sigma weight residual 109.16 117.38 -8.22 1.29e+00 6.01e-01 4.06e+01 angle pdb=" N ASN N 625 " pdb=" CA ASN N 625 " pdb=" CB ASN N 625 " ideal model delta sigma weight residual 111.15 104.15 7.00 1.46e+00 4.69e-01 2.30e+01 angle pdb=" C ASN N 624 " pdb=" N ASN N 625 " pdb=" CA ASN N 625 " ideal model delta sigma weight residual 121.52 113.31 8.21 1.74e+00 3.30e-01 2.23e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " ideal model delta sigma weight residual 111.36 103.79 7.57 1.82e+00 3.02e-01 1.73e+01 ... (remaining 40965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15167 17.92 - 35.84: 1453 35.84 - 53.77: 261 53.77 - 71.69: 48 71.69 - 89.61: 32 Dihedral angle restraints: 16961 sinusoidal: 6738 harmonic: 10223 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -170.36 84.36 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -169.89 83.89 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS D 134 " pdb=" SG CYS D 134 " pdb=" SG CYS D 194 " pdb=" CB CYS D 194 " ideal model delta sinusoidal sigma weight residual 93.00 175.90 -82.90 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 16958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 4966 0.227 - 0.454: 23 0.454 - 0.681: 4 0.681 - 0.908: 1 0.908 - 1.135: 1 Chirality restraints: 4995 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" C1 NAG r 1 " pdb=" ND2 ASN G 88 " pdb=" C2 NAG r 1 " pdb=" O5 NAG r 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG N 703 " pdb=" ND2 ASN N 625 " pdb=" C2 NAG N 703 " pdb=" O5 NAG N 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.11e+01 ... (remaining 4992 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 448 " -0.019 2.00e-02 2.50e+03 7.03e-02 6.18e+01 pdb=" CG ASN A 448 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 448 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 448 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 625 " -0.003 2.00e-02 2.50e+03 5.30e-02 3.51e+01 pdb=" CG ASN N 625 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN N 625 " 0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN N 625 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG N 703 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.051 2.00e-02 2.50e+03 4.72e-02 2.78e+01 pdb=" CG ASN A 88 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.053 2.00e-02 2.50e+03 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 708 2.66 - 3.22: 28764 3.22 - 3.78: 43922 3.78 - 4.34: 58196 4.34 - 4.90: 93408 Nonbonded interactions: 224998 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OE1 GLN D 24 " model vdw 2.103 3.040 nonbonded pdb=" OD1 ASN F 133 " pdb=" NH1 ARG F 155 " model vdw 2.119 3.120 nonbonded pdb=" O PRO X 135 " pdb=" NE2 GLN Y 124 " model vdw 2.137 3.120 nonbonded pdb=" O LEU D 106 " pdb=" OH TYR D 140 " model vdw 2.149 3.040 nonbonded pdb=" O CYS K 134 " pdb=" OG SER K 177 " model vdw 2.151 3.040 ... (remaining 224993 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 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = (chain 'S' and resid 1 through 213) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' 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 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'L' 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)) } ncs_group { reference = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'k' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.470 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 0.099 30292 Z= 0.231 Angle : 0.857 22.811 41479 Z= 0.379 Chirality : 0.059 1.135 4995 Planarity : 0.005 0.060 5045 Dihedral : 14.286 89.611 10217 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.88 (0.14), residues: 3481 helix: -1.20 (0.25), residues: 406 sheet: -0.53 (0.17), residues: 982 loop : -1.66 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 56 TYR 0.023 0.001 TYR X 111 PHE 0.009 0.001 PHE Y 118 TRP 0.039 0.002 TRP G 69 HIS 0.014 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (30104) covalent geometry : angle 0.73540 / 0.35 (40970) SS BOND : bond 0.00324 / 0.23 ( 52) SS BOND : angle 1.40030 / 0.95 ( 104) hydrogen bonds : bond 0.27878 / 18.64 ( 674) hydrogen bonds : angle 10.51430 / 7.26 ( 1821) Misc. bond : bond 0.00344 / 0.18 ( 1) link_ALPHA1-2 : bond 0.00148 / 0.07 ( 3) link_ALPHA1-2 : angle 2.26070 / 1.27 ( 9) link_ALPHA1-3 : bond 0.00482 / 0.31 ( 9) link_ALPHA1-3 : angle 1.76947 / 1.14 ( 27) link_ALPHA1-6 : bond 0.00356 / 0.22 ( 9) link_ALPHA1-6 : angle 1.85411 / 1.22 ( 27) link_BETA1-4 : bond 0.00633 / 0.32 ( 41) link_BETA1-4 : angle 1.78992 / 1.22 ( 123) link_NAG-ASN : bond 0.00989 / 0.72 ( 73) link_NAG-ASN : angle 5.83586 / 4.12 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8767 (ppp) cc_final: 0.8336 (tmm) REVERT: A 318 TYR cc_start: 0.7790 (m-80) cc_final: 0.7539 (m-80) REVERT: D 175 LEU cc_start: 0.9110 (tp) cc_final: 0.8886 (tp) REVERT: F 66 HIS cc_start: 0.8263 (m90) cc_final: 0.7855 (m90) REVERT: G 117 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8374 (tptm) REVERT: G 282 LYS cc_start: 0.8971 (mptt) cc_final: 0.8752 (mmtm) REVERT: J 32 TYR cc_start: 0.8975 (m-10) cc_final: 0.8652 (m-10) REVERT: K 204 PRO cc_start: 0.6563 (Cg_exo) cc_final: 0.6315 (Cg_endo) REVERT: X 70 MET cc_start: 0.6154 (ppp) cc_final: 0.5749 (ptp) REVERT: X 94 TYR cc_start: 0.6717 (m-80) cc_final: 0.4271 (m-80) REVERT: X 109 GLN cc_start: 0.8843 (mp10) cc_final: 0.8308 (mp10) REVERT: B 520 PHE cc_start: 0.7775 (m-80) cc_final: 0.7480 (m-10) outliers start: 5 outliers final: 1 residues processed: 215 average time/residue: 0.1855 time to fit residues: 64.4843 Evaluate side-chains 156 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 146 ASN C 3 GLN C 6 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN F 490 GLN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 39 GLN J 62 GLN K 38 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** M 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065030 restraints weight = 126671.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.065098 restraints weight = 82518.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065497 restraints weight = 75576.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065681 restraints weight = 63958.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065742 restraints weight = 59569.784| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30292 Z= 0.211 Angle : 0.766 20.100 41479 Z= 0.362 Chirality : 0.049 0.405 4995 Planarity : 0.005 0.061 5045 Dihedral : 5.039 29.537 3764 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.16 % Allowed : 6.92 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.85 (0.14), residues: 3481 helix: -0.72 (0.25), residues: 412 sheet: -0.64 (0.16), residues: 1020 loop : -1.69 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 155 TYR 0.020 0.002 TYR X 111 PHE 0.025 0.002 PHE M 651 TRP 0.020 0.002 TRP F 479 HIS 0.008 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (30104) covalent geometry : angle 0.68375 / 0.34 (40970) SS BOND : bond 0.00398 / 0.27 ( 52) SS BOND : angle 1.31856 / 0.90 ( 104) hydrogen bonds : bond 0.05822 / 3.89 ( 674) hydrogen bonds : angle 7.50555 / 5.13 ( 1821) Misc. bond : bond 0.00103 / 0.05 ( 1) link_ALPHA1-2 : bond 0.00309 / 0.13 ( 3) link_ALPHA1-2 : angle 1.93310 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00548 / 0.35 ( 9) link_ALPHA1-3 : angle 1.90091 / 1.22 ( 27) link_ALPHA1-6 : bond 0.00351 / 0.24 ( 9) link_ALPHA1-6 : angle 2.10231 / 1.37 ( 27) link_BETA1-4 : bond 0.00500 / 0.28 ( 41) link_BETA1-4 : angle 1.60877 / 1.08 ( 123) link_NAG-ASN : bond 0.00713 / 0.51 ( 73) link_NAG-ASN : angle 4.48523 / 3.20 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8827 (mtm) cc_final: 0.8385 (mtm) REVERT: A 104 MET cc_start: 0.8874 (ppp) cc_final: 0.8531 (tmm) REVERT: C 36 TRP cc_start: 0.9101 (m100) cc_final: 0.8827 (m-10) REVERT: D 91 TYR cc_start: 0.7893 (m-80) cc_final: 0.7664 (m-80) REVERT: F 66 HIS cc_start: 0.8351 (m90) cc_final: 0.7936 (m90) REVERT: F 434 MET cc_start: 0.8520 (tmm) cc_final: 0.8195 (tmm) REVERT: G 104 MET cc_start: 0.8966 (tmm) cc_final: 0.8643 (tmm) REVERT: G 117 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8576 (tptm) REVERT: J 72 ASP cc_start: 0.8611 (m-30) cc_final: 0.8190 (m-30) REVERT: K 204 PRO cc_start: 0.6587 (Cg_exo) cc_final: 0.6339 (Cg_endo) REVERT: S 100 ASP cc_start: 0.8390 (p0) cc_final: 0.8170 (p0) REVERT: U 81 GLU cc_start: 0.6595 (pp20) cc_final: 0.5986 (pm20) REVERT: X 70 MET cc_start: 0.6004 (ppp) cc_final: 0.5705 (ppp) REVERT: X 109 GLN cc_start: 0.8884 (mp10) cc_final: 0.8457 (mp10) REVERT: Y 165 GLU cc_start: 0.7937 (tp30) cc_final: 0.7695 (tp30) REVERT: B 520 PHE cc_start: 0.7810 (m-80) cc_final: 0.7451 (m-10) REVERT: B 530 MET cc_start: 0.8022 (ttm) cc_final: 0.7777 (ttp) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 0.1945 time to fit residues: 63.9600 Evaluate side-chains 160 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 274 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN C 3 GLN C 58 ASN F 490 GLN G 183 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.082343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066293 restraints weight = 125085.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066149 restraints weight = 83595.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066682 restraints weight = 79550.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066828 restraints weight = 66544.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067223 restraints weight = 59601.401| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30292 Z= 0.156 Angle : 0.714 20.303 41479 Z= 0.333 Chirality : 0.048 0.386 4995 Planarity : 0.004 0.056 5045 Dihedral : 4.873 30.323 3764 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.80 (0.14), residues: 3481 helix: -0.50 (0.26), residues: 395 sheet: -0.61 (0.16), residues: 1016 loop : -1.69 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 61 TYR 0.021 0.001 TYR X 111 PHE 0.029 0.001 PHE M 651 TRP 0.016 0.001 TRP M 628 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (30104) covalent geometry : angle 0.63361 / 0.31 (40970) SS BOND : bond 0.00533 / 0.33 ( 52) SS BOND : angle 1.24087 / 0.86 ( 104) hydrogen bonds : bond 0.04609 / 3.08 ( 674) hydrogen bonds : angle 6.64097 / 4.52 ( 1821) Misc. bond : bond 0.00044 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00215 / 0.11 ( 3) link_ALPHA1-2 : angle 1.88084 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00519 / 0.30 ( 9) link_ALPHA1-3 : angle 1.64811 / 1.07 ( 27) link_ALPHA1-6 : bond 0.00384 / 0.27 ( 9) link_ALPHA1-6 : angle 1.89620 / 1.27 ( 27) link_BETA1-4 : bond 0.00509 / 0.31 ( 41) link_BETA1-4 : angle 1.56838 / 1.05 ( 123) link_NAG-ASN : bond 0.00742 / 0.51 ( 73) link_NAG-ASN : angle 4.29215 / 3.08 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8816 (ppp) cc_final: 0.8440 (tmm) REVERT: C 36 TRP cc_start: 0.9048 (m100) cc_final: 0.8814 (m-10) REVERT: D 175 LEU cc_start: 0.9263 (tp) cc_final: 0.9025 (tp) REVERT: F 66 HIS cc_start: 0.8393 (m90) cc_final: 0.7984 (m90) REVERT: F 373 MET cc_start: 0.8618 (tpp) cc_final: 0.8300 (tpp) REVERT: F 434 MET cc_start: 0.8524 (tmm) cc_final: 0.8321 (tmm) REVERT: J 72 ASP cc_start: 0.8702 (m-30) cc_final: 0.8141 (m-30) REVERT: K 204 PRO cc_start: 0.6595 (Cg_exo) cc_final: 0.6330 (Cg_endo) REVERT: S 100 ASP cc_start: 0.8418 (p0) cc_final: 0.8083 (p0) REVERT: U 96 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7585 (mm-30) REVERT: X 70 MET cc_start: 0.5800 (ppp) cc_final: 0.5600 (ppp) REVERT: X 191 SER cc_start: 0.8068 (p) cc_final: 0.7733 (m) REVERT: Y 165 GLU cc_start: 0.7921 (tp30) cc_final: 0.7663 (tp30) REVERT: B 520 PHE cc_start: 0.7794 (m-80) cc_final: 0.7442 (m-10) REVERT: B 530 MET cc_start: 0.8042 (ttm) cc_final: 0.7696 (ttp) outliers start: 4 outliers final: 0 residues processed: 210 average time/residue: 0.1977 time to fit residues: 66.2578 Evaluate side-chains 156 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 289 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 202 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 338 optimal weight: 2.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN C 3 GLN F 478 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN M 624 ASN B 656 ASN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065167 restraints weight = 124446.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065541 restraints weight = 82391.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065761 restraints weight = 75652.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065956 restraints weight = 66970.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066101 restraints weight = 58155.980| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30292 Z= 0.210 Angle : 0.761 20.156 41479 Z= 0.355 Chirality : 0.049 0.394 4995 Planarity : 0.005 0.056 5045 Dihedral : 5.043 27.640 3764 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.87 (0.14), residues: 3481 helix: -0.61 (0.25), residues: 405 sheet: -0.68 (0.16), residues: 1021 loop : -1.71 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 142 TYR 0.023 0.002 TYR X 111 PHE 0.025 0.002 PHE M 651 TRP 0.043 0.002 TRP M 631 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (30104) covalent geometry : angle 0.68115 / 0.34 (40970) SS BOND : bond 0.00403 / 0.28 ( 52) SS BOND : angle 1.42262 / 0.95 ( 104) hydrogen bonds : bond 0.04504 / 2.99 ( 674) hydrogen bonds : angle 6.48822 / 4.43 ( 1821) Misc. bond : bond 0.00008 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00113 / 0.05 ( 3) link_ALPHA1-2 : angle 1.92462 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00377 / 0.19 ( 9) link_ALPHA1-3 : angle 1.78050 / 1.15 ( 27) link_ALPHA1-6 : bond 0.00294 / 0.19 ( 9) link_ALPHA1-6 : angle 1.95312 / 1.29 ( 27) link_BETA1-4 : bond 0.00430 / 0.26 ( 41) link_BETA1-4 : angle 1.60183 / 1.08 ( 123) link_NAG-ASN : bond 0.00762 / 0.53 ( 73) link_NAG-ASN : angle 4.39875 / 3.13 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9080 (mtp) cc_final: 0.8779 (mtm) REVERT: A 104 MET cc_start: 0.8906 (ppp) cc_final: 0.8479 (tmm) REVERT: C 36 TRP cc_start: 0.9126 (m100) cc_final: 0.8883 (m-10) REVERT: D 165 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7980 (tm-30) REVERT: F 100 MET cc_start: 0.7744 (mtp) cc_final: 0.7413 (mtm) REVERT: F 373 MET cc_start: 0.8763 (tpp) cc_final: 0.7787 (mmt) REVERT: F 434 MET cc_start: 0.8541 (tmm) cc_final: 0.7987 (tmm) REVERT: K 204 PRO cc_start: 0.6545 (Cg_exo) cc_final: 0.6275 (Cg_endo) REVERT: U 140 TYR cc_start: 0.6184 (t80) cc_final: 0.5624 (t80) REVERT: X 94 TYR cc_start: 0.5565 (m-80) cc_final: 0.5309 (m-80) REVERT: X 191 SER cc_start: 0.8053 (p) cc_final: 0.7782 (m) outliers start: 4 outliers final: 0 residues processed: 198 average time/residue: 0.1919 time to fit residues: 61.5589 Evaluate side-chains 150 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 195 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 194 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 124 GLN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN S 3 GLN S 59 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.083167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066964 restraints weight = 122961.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067366 restraints weight = 79727.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067622 restraints weight = 69332.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067977 restraints weight = 59871.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068005 restraints weight = 53395.903| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30292 Z= 0.124 Angle : 0.690 20.226 41479 Z= 0.321 Chirality : 0.048 0.393 4995 Planarity : 0.004 0.054 5045 Dihedral : 4.790 31.549 3764 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.73 (0.14), residues: 3481 helix: -0.37 (0.26), residues: 397 sheet: -0.62 (0.16), residues: 1022 loop : -1.63 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 61 TYR 0.023 0.001 TYR X 111 PHE 0.017 0.001 PHE M 651 TRP 0.029 0.001 TRP M 631 HIS 0.005 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30104) covalent geometry : angle 0.61765 / 0.30 (40970) SS BOND : bond 0.00368 / 0.26 ( 52) SS BOND : angle 1.30826 / 0.91 ( 104) hydrogen bonds : bond 0.03909 / 2.60 ( 674) hydrogen bonds : angle 6.05698 / 4.12 ( 1821) Misc. bond : bond 0.00040 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00148 / 0.07 ( 3) link_ALPHA1-2 : angle 1.77124 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00579 / 0.35 ( 9) link_ALPHA1-3 : angle 1.57125 / 1.03 ( 27) link_ALPHA1-6 : bond 0.00359 / 0.23 ( 9) link_ALPHA1-6 : angle 1.78256 / 1.18 ( 27) link_BETA1-4 : bond 0.00466 / 0.28 ( 41) link_BETA1-4 : angle 1.48060 / 0.99 ( 123) link_NAG-ASN : bond 0.00707 / 0.50 ( 73) link_NAG-ASN : angle 4.00676 / 2.87 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9004 (mtp) cc_final: 0.8546 (mtm) REVERT: A 104 MET cc_start: 0.8803 (ppp) cc_final: 0.8497 (tmm) REVERT: C 36 TRP cc_start: 0.9054 (m100) cc_final: 0.8820 (m-10) REVERT: F 66 HIS cc_start: 0.8175 (m90) cc_final: 0.7817 (m90) REVERT: F 100 MET cc_start: 0.7581 (mtp) cc_final: 0.7249 (mtm) REVERT: F 373 MET cc_start: 0.8769 (tpp) cc_final: 0.7717 (mmt) REVERT: F 434 MET cc_start: 0.8573 (tmm) cc_final: 0.7983 (tmm) REVERT: K 204 PRO cc_start: 0.6539 (Cg_exo) cc_final: 0.6266 (Cg_endo) REVERT: S 100 ASP cc_start: 0.8318 (p0) cc_final: 0.7924 (p0) REVERT: U 140 TYR cc_start: 0.6355 (t80) cc_final: 0.6050 (t80) REVERT: X 191 SER cc_start: 0.8152 (p) cc_final: 0.7839 (m) REVERT: B 530 MET cc_start: 0.8020 (ttm) cc_final: 0.7744 (ttp) REVERT: N 530 MET cc_start: 0.7920 (mmm) cc_final: 0.7003 (tmm) outliers start: 4 outliers final: 0 residues processed: 206 average time/residue: 0.1952 time to fit residues: 65.0603 Evaluate side-chains 152 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN C 3 GLN D 138 ASN F 478 ASN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN S 3 GLN U 79 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.082618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066423 restraints weight = 124690.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066613 restraints weight = 85369.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067035 restraints weight = 73800.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067173 restraints weight = 63705.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067235 restraints weight = 59334.121| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30292 Z= 0.148 Angle : 0.701 20.055 41479 Z= 0.325 Chirality : 0.048 0.505 4995 Planarity : 0.004 0.055 5045 Dihedral : 4.779 29.352 3764 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.70 (0.14), residues: 3481 helix: -0.31 (0.26), residues: 395 sheet: -0.49 (0.16), residues: 990 loop : -1.67 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.023 0.001 TYR X 111 PHE 0.014 0.001 PHE M 651 TRP 0.038 0.001 TRP A 69 HIS 0.005 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (30104) covalent geometry : angle 0.62498 / 0.31 (40970) SS BOND : bond 0.00353 / 0.25 ( 52) SS BOND : angle 1.23783 / 0.85 ( 104) hydrogen bonds : bond 0.03861 / 2.55 ( 674) hydrogen bonds : angle 5.98318 / 4.08 ( 1821) Misc. bond : bond 0.00020 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00182 / 0.09 ( 3) link_ALPHA1-2 : angle 1.77271 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00551 / 0.33 ( 9) link_ALPHA1-3 : angle 1.63605 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00393 / 0.27 ( 9) link_ALPHA1-6 : angle 1.87938 / 1.25 ( 27) link_BETA1-4 : bond 0.00472 / 0.27 ( 41) link_BETA1-4 : angle 1.46773 / 0.99 ( 123) link_NAG-ASN : bond 0.00677 / 0.48 ( 73) link_NAG-ASN : angle 4.14969 / 2.98 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8970 (mtp) cc_final: 0.8559 (mtm) REVERT: A 104 MET cc_start: 0.8898 (ppp) cc_final: 0.8584 (tmm) REVERT: C 36 TRP cc_start: 0.9070 (m100) cc_final: 0.8828 (m-10) REVERT: D 4 MET cc_start: 0.8593 (tpp) cc_final: 0.8313 (tpt) REVERT: F 100 MET cc_start: 0.7645 (mtp) cc_final: 0.7299 (mtm) REVERT: F 373 MET cc_start: 0.8799 (tpp) cc_final: 0.7813 (mmt) REVERT: F 434 MET cc_start: 0.8541 (tmm) cc_final: 0.7982 (tmm) REVERT: G 69 TRP cc_start: 0.8141 (m100) cc_final: 0.7512 (m100) REVERT: G 117 LYS cc_start: 0.8520 (tptt) cc_final: 0.8181 (tptm) REVERT: J 72 ASP cc_start: 0.8674 (m-30) cc_final: 0.8295 (m-30) REVERT: S 100 ASP cc_start: 0.8356 (p0) cc_final: 0.7985 (p0) REVERT: U 140 TYR cc_start: 0.6290 (t80) cc_final: 0.5984 (t80) REVERT: X 191 SER cc_start: 0.7957 (p) cc_final: 0.7455 (m) REVERT: B 530 MET cc_start: 0.8015 (ttm) cc_final: 0.7656 (ttp) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.1805 time to fit residues: 58.1608 Evaluate side-chains 154 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 240 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN C 3 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.080808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064644 restraints weight = 126487.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064686 restraints weight = 86732.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065082 restraints weight = 75872.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065213 restraints weight = 68821.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065282 restraints weight = 62955.714| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30292 Z= 0.239 Angle : 0.782 19.845 41479 Z= 0.368 Chirality : 0.050 0.407 4995 Planarity : 0.005 0.060 5045 Dihedral : 5.163 32.372 3764 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.89 (0.14), residues: 3481 helix: -0.56 (0.26), residues: 403 sheet: -0.63 (0.16), residues: 981 loop : -1.76 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 56 TYR 0.025 0.002 TYR X 111 PHE 0.016 0.002 PHE S 122 TRP 0.044 0.002 TRP A 69 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (30104) covalent geometry : angle 0.70933 / 0.35 (40970) SS BOND : bond 0.00374 / 0.25 ( 52) SS BOND : angle 1.58686 / 1.08 ( 104) hydrogen bonds : bond 0.04372 / 2.92 ( 674) hydrogen bonds : angle 6.19417 / 4.23 ( 1821) Misc. bond : bond 0.00064 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00288 / 0.13 ( 3) link_ALPHA1-2 : angle 1.90656 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00466 / 0.28 ( 9) link_ALPHA1-3 : angle 1.90247 / 1.24 ( 27) link_ALPHA1-6 : bond 0.00257 / 0.18 ( 9) link_ALPHA1-6 : angle 2.00613 / 1.32 ( 27) link_BETA1-4 : bond 0.00430 / 0.26 ( 41) link_BETA1-4 : angle 1.57749 / 1.07 ( 123) link_NAG-ASN : bond 0.00688 / 0.49 ( 73) link_NAG-ASN : angle 4.25792 / 3.04 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9001 (mtp) cc_final: 0.8731 (mtm) REVERT: A 104 MET cc_start: 0.8998 (ppp) cc_final: 0.8565 (tmm) REVERT: A 317 PHE cc_start: 0.7596 (t80) cc_final: 0.7337 (t80) REVERT: C 36 TRP cc_start: 0.9157 (m100) cc_final: 0.8912 (m-10) REVERT: D 4 MET cc_start: 0.8801 (tpp) cc_final: 0.8513 (tpt) REVERT: D 165 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 175 LEU cc_start: 0.9124 (tp) cc_final: 0.8793 (tp) REVERT: F 100 MET cc_start: 0.7810 (mtp) cc_final: 0.7556 (mtm) REVERT: F 373 MET cc_start: 0.9104 (mmt) cc_final: 0.8011 (mmt) REVERT: F 434 MET cc_start: 0.8530 (tmm) cc_final: 0.7953 (tmm) REVERT: G 69 TRP cc_start: 0.8247 (m100) cc_final: 0.7604 (m100) REVERT: G 117 LYS cc_start: 0.8548 (tptt) cc_final: 0.8201 (tptm) REVERT: U 140 TYR cc_start: 0.6493 (t80) cc_final: 0.6149 (t80) REVERT: X 191 SER cc_start: 0.8088 (p) cc_final: 0.7622 (m) REVERT: B 530 MET cc_start: 0.8158 (ttm) cc_final: 0.7948 (ttp) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.1774 time to fit residues: 55.8407 Evaluate side-chains 138 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 325 optimal weight: 0.8980 chunk 242 optimal weight: 0.0770 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 294 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN G 99 ASN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 37 GLN K 147 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066382 restraints weight = 124811.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066603 restraints weight = 83302.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066995 restraints weight = 72973.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067191 restraints weight = 61695.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067261 restraints weight = 57232.068| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30292 Z= 0.126 Angle : 0.706 20.299 41479 Z= 0.328 Chirality : 0.048 0.438 4995 Planarity : 0.004 0.059 5045 Dihedral : 4.851 28.775 3764 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.13 % Allowed : 1.29 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.76 (0.14), residues: 3481 helix: -0.38 (0.26), residues: 395 sheet: -0.55 (0.16), residues: 1020 loop : -1.71 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 633 TYR 0.017 0.001 TYR F 217 PHE 0.012 0.001 PHE M 651 TRP 0.050 0.001 TRP A 69 HIS 0.005 0.001 HIS G 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (30104) covalent geometry : angle 0.63578 / 0.31 (40970) SS BOND : bond 0.00387 / 0.26 ( 52) SS BOND : angle 1.37545 / 0.93 ( 104) hydrogen bonds : bond 0.03741 / 2.47 ( 674) hydrogen bonds : angle 5.84620 / 3.98 ( 1821) Misc. bond : bond 0.00007 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00166 / 0.08 ( 3) link_ALPHA1-2 : angle 1.77564 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00640 / 0.40 ( 9) link_ALPHA1-3 : angle 1.58315 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00502 / 0.33 ( 9) link_ALPHA1-6 : angle 1.81828 / 1.21 ( 27) link_BETA1-4 : bond 0.00461 / 0.27 ( 41) link_BETA1-4 : angle 1.45101 / 0.97 ( 123) link_NAG-ASN : bond 0.00680 / 0.48 ( 73) link_NAG-ASN : angle 3.97344 / 2.83 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8939 (mtp) cc_final: 0.8601 (mtm) REVERT: A 104 MET cc_start: 0.8942 (ppp) cc_final: 0.8561 (tmm) REVERT: A 111 LEU cc_start: 0.9222 (mm) cc_final: 0.8890 (mt) REVERT: C 36 TRP cc_start: 0.9053 (m100) cc_final: 0.8836 (m-10) REVERT: D 4 MET cc_start: 0.8683 (tpp) cc_final: 0.8364 (tpt) REVERT: F 100 MET cc_start: 0.7768 (mtp) cc_final: 0.7413 (mtm) REVERT: F 373 MET cc_start: 0.9102 (mmt) cc_final: 0.8362 (tpp) REVERT: F 434 MET cc_start: 0.8475 (tmm) cc_final: 0.7989 (tmm) REVERT: G 69 TRP cc_start: 0.8012 (m100) cc_final: 0.7638 (m100) REVERT: G 117 LYS cc_start: 0.8502 (tptt) cc_final: 0.8158 (tptm) REVERT: J 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8175 (m-30) REVERT: K 14 SER cc_start: 0.8487 (m) cc_final: 0.8073 (m) REVERT: U 140 TYR cc_start: 0.6277 (t80) cc_final: 0.5990 (t80) REVERT: X 134 PHE cc_start: 0.5505 (m-80) cc_final: 0.4972 (m-80) REVERT: X 191 SER cc_start: 0.8070 (p) cc_final: 0.7633 (m) REVERT: Y 165 GLU cc_start: 0.7956 (tp30) cc_final: 0.7737 (tp30) REVERT: B 530 MET cc_start: 0.7975 (ttm) cc_final: 0.7671 (ttp) REVERT: N 530 MET cc_start: 0.7829 (mmm) cc_final: 0.6884 (tmm) outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.1909 time to fit residues: 64.9209 Evaluate side-chains 156 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 281 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 144 optimal weight: 0.0670 chunk 322 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 303 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN F 478 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065952 restraints weight = 125174.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066137 restraints weight = 82343.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066526 restraints weight = 72413.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066686 restraints weight = 62274.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066767 restraints weight = 58121.031| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30292 Z= 0.143 Angle : 0.717 19.950 41479 Z= 0.332 Chirality : 0.048 0.408 4995 Planarity : 0.004 0.061 5045 Dihedral : 4.839 32.788 3764 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.10 % Allowed : 0.74 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.75 (0.14), residues: 3481 helix: -0.31 (0.26), residues: 395 sheet: -0.46 (0.16), residues: 996 loop : -1.75 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 633 TYR 0.015 0.001 TYR J 176 PHE 0.016 0.001 PHE M 651 TRP 0.040 0.001 TRP F 479 HIS 0.011 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (30104) covalent geometry : angle 0.64173 / 0.32 (40970) SS BOND : bond 0.00351 / 0.24 ( 52) SS BOND : angle 1.30907 / 0.86 ( 104) hydrogen bonds : bond 0.03728 / 2.46 ( 674) hydrogen bonds : angle 5.77025 / 3.94 ( 1821) Misc. bond : bond 0.00016 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00164 / 0.08 ( 3) link_ALPHA1-2 : angle 1.80201 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00531 / 0.32 ( 9) link_ALPHA1-3 : angle 1.61334 / 1.05 ( 27) link_ALPHA1-6 : bond 0.00434 / 0.30 ( 9) link_ALPHA1-6 : angle 1.82640 / 1.23 ( 27) link_BETA1-4 : bond 0.00451 / 0.26 ( 41) link_BETA1-4 : angle 1.45310 / 0.98 ( 123) link_NAG-ASN : bond 0.00653 / 0.47 ( 73) link_NAG-ASN : angle 4.16643 / 2.94 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8923 (mtp) cc_final: 0.8556 (mtm) REVERT: A 111 LEU cc_start: 0.9215 (mm) cc_final: 0.8901 (mt) REVERT: A 175 LEU cc_start: 0.9057 (tp) cc_final: 0.8819 (tp) REVERT: C 36 TRP cc_start: 0.9087 (m100) cc_final: 0.8839 (m-10) REVERT: D 4 MET cc_start: 0.8694 (tpp) cc_final: 0.8294 (tpt) REVERT: D 124 GLN cc_start: 0.7594 (tt0) cc_final: 0.7221 (tt0) REVERT: F 100 MET cc_start: 0.7738 (mtp) cc_final: 0.7401 (mtm) REVERT: F 373 MET cc_start: 0.9094 (mmt) cc_final: 0.8362 (tpp) REVERT: F 434 MET cc_start: 0.8540 (tmm) cc_final: 0.8021 (tmm) REVERT: G 117 LYS cc_start: 0.8462 (tptt) cc_final: 0.8080 (tptm) REVERT: S 100 ASP cc_start: 0.8314 (p0) cc_final: 0.7943 (p0) REVERT: U 140 TYR cc_start: 0.6385 (t80) cc_final: 0.6066 (t80) REVERT: X 191 SER cc_start: 0.8149 (p) cc_final: 0.7684 (m) REVERT: Y 165 GLU cc_start: 0.7978 (tp30) cc_final: 0.7751 (tp30) REVERT: M 626 MET cc_start: 0.8243 (tpp) cc_final: 0.7992 (tpt) REVERT: M 630 GLU cc_start: 0.7838 (pp20) cc_final: 0.7305 (pp20) REVERT: B 530 MET cc_start: 0.8012 (ttm) cc_final: 0.7753 (ttp) outliers start: 3 outliers final: 0 residues processed: 197 average time/residue: 0.1740 time to fit residues: 56.3092 Evaluate side-chains 158 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 229 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 281 optimal weight: 0.7980 chunk 9 optimal weight: 0.0010 chunk 168 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 chunk 244 optimal weight: 0.0060 chunk 221 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 69 GLN D 137 ASN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.083672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067384 restraints weight = 124195.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067426 restraints weight = 85056.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067853 restraints weight = 73493.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068002 restraints weight = 65249.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068107 restraints weight = 59992.713| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30292 Z= 0.111 Angle : 0.690 20.162 41479 Z= 0.319 Chirality : 0.048 0.402 4995 Planarity : 0.004 0.059 5045 Dihedral : 4.646 32.577 3764 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.10 % Allowed : 0.45 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.66 (0.14), residues: 3481 helix: -0.20 (0.26), residues: 395 sheet: -0.48 (0.16), residues: 1006 loop : -1.65 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 56 TYR 0.013 0.001 TYR D 49 PHE 0.023 0.001 PHE A 317 TRP 0.035 0.001 TRP A 69 HIS 0.011 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (30104) covalent geometry : angle 0.62032 / 0.30 (40970) SS BOND : bond 0.00362 / 0.24 ( 52) SS BOND : angle 1.20266 / 0.80 ( 104) hydrogen bonds : bond 0.03403 / 2.24 ( 674) hydrogen bonds : angle 5.53392 / 3.78 ( 1821) Misc. bond : bond 0.00044 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00142 / 0.07 ( 3) link_ALPHA1-2 : angle 1.71239 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00605 / 0.37 ( 9) link_ALPHA1-3 : angle 1.50283 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00502 / 0.33 ( 9) link_ALPHA1-6 : angle 1.71692 / 1.16 ( 27) link_BETA1-4 : bond 0.00466 / 0.28 ( 41) link_BETA1-4 : angle 1.39613 / 0.93 ( 123) link_NAG-ASN : bond 0.00691 / 0.49 ( 73) link_NAG-ASN : angle 3.96416 / 2.80 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8722 (mtp) cc_final: 0.8365 (mtm) REVERT: A 111 LEU cc_start: 0.9188 (mm) cc_final: 0.8866 (mt) REVERT: A 317 PHE cc_start: 0.7572 (t80) cc_final: 0.7363 (t80) REVERT: C 36 TRP cc_start: 0.8975 (m100) cc_final: 0.8755 (m-10) REVERT: C 71 TRP cc_start: 0.7408 (p-90) cc_final: 0.6781 (p-90) REVERT: C 72 ASP cc_start: 0.8335 (p0) cc_final: 0.7593 (p0) REVERT: C 83 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7473 (mpt180) REVERT: D 4 MET cc_start: 0.8626 (tpp) cc_final: 0.8242 (tpp) REVERT: D 116 PHE cc_start: 0.7558 (m-10) cc_final: 0.7341 (m-10) REVERT: D 124 GLN cc_start: 0.7497 (tt0) cc_final: 0.7223 (tt0) REVERT: F 100 MET cc_start: 0.7647 (mtp) cc_final: 0.7263 (mtm) REVERT: F 373 MET cc_start: 0.9033 (mmt) cc_final: 0.8452 (tpp) REVERT: F 434 MET cc_start: 0.8487 (tmm) cc_final: 0.8007 (tmm) REVERT: G 69 TRP cc_start: 0.7943 (m100) cc_final: 0.7634 (m100) REVERT: S 100 ASP cc_start: 0.8153 (p0) cc_final: 0.7759 (p0) REVERT: U 81 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7423 (mp0) REVERT: U 140 TYR cc_start: 0.6280 (t80) cc_final: 0.5816 (t80) REVERT: X 134 PHE cc_start: 0.5467 (m-80) cc_final: 0.4963 (m-80) REVERT: X 178 PHE cc_start: 0.6235 (m-10) cc_final: 0.6033 (m-10) REVERT: X 191 SER cc_start: 0.8252 (p) cc_final: 0.7839 (m) REVERT: Y 165 GLU cc_start: 0.7958 (tp30) cc_final: 0.7743 (tp30) REVERT: M 626 MET cc_start: 0.8188 (tpp) cc_final: 0.7704 (tpt) REVERT: B 530 MET cc_start: 0.7909 (ttm) cc_final: 0.7551 (ttp) outliers start: 3 outliers final: 2 residues processed: 195 average time/residue: 0.1729 time to fit residues: 55.8271 Evaluate side-chains 163 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 73 optimal weight: 0.0870 chunk 330 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN F 478 ASN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 62 GLN K 152 ASN S 164 HIS ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 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 = 0.3679 r_free = 0.3679 target = 0.083893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068505 restraints weight = 131633.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068434 restraints weight = 121644.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068754 restraints weight = 97850.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068929 restraints weight = 87583.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069098 restraints weight = 78714.014| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30292 Z= 0.116 Angle : 0.681 19.967 41479 Z= 0.316 Chirality : 0.048 0.399 4995 Planarity : 0.004 0.062 5045 Dihedral : 4.564 32.346 3764 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.59 (0.14), residues: 3481 helix: -0.15 (0.26), residues: 395 sheet: -0.38 (0.16), residues: 999 loop : -1.63 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 633 TYR 0.012 0.001 TYR U 36 PHE 0.020 0.001 PHE A 317 TRP 0.032 0.001 TRP A 69 HIS 0.010 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (30104) covalent geometry : angle 0.61342 / 0.30 (40970) SS BOND : bond 0.00334 / 0.23 ( 52) SS BOND : angle 1.17924 / 0.78 ( 104) hydrogen bonds : bond 0.03361 / 2.20 ( 674) hydrogen bonds : angle 5.42552 / 3.70 ( 1821) Misc. bond : bond 0.00022 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00136 / 0.07 ( 3) link_ALPHA1-2 : angle 1.70786 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00550 / 0.33 ( 9) link_ALPHA1-3 : angle 1.52715 / 0.99 ( 27) link_ALPHA1-6 : bond 0.00468 / 0.32 ( 9) link_ALPHA1-6 : angle 1.70314 / 1.15 ( 27) link_BETA1-4 : bond 0.00453 / 0.27 ( 41) link_BETA1-4 : angle 1.39519 / 0.94 ( 123) link_NAG-ASN : bond 0.00658 / 0.47 ( 73) link_NAG-ASN : angle 3.86856 / 2.74 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.64 seconds wall clock time: 71 minutes 30.32 seconds (4290.32 seconds total)