Starting phenix.real_space_refine on Sat Jul 4 13:15:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dto_27706/07_2026/8dto_27706.cif" } resolution = 3.57 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= 0.001 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12990 2.51 5 N 3366 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 20923 Number of models: 1 Model: "" Number of chains: 54 Chain: "E" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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: "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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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: "a" 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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "g" 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: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" 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: "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: 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: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "u" 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: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.34, per 1000 atoms: 0.21 Number of scatterers: 20923 At special positions: 0 Unit cell: (163.08, 157.68, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4435 8.00 N 3366 7.00 C 12990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 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 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 444 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA p 3 " - " MAN p 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 5 " " BMA S 3 " - " MAN S 7 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 5 " " BMA f 3 " - " MAN f 7 " " BMA h 3 " - " MAN h 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 5 " " BMA t 3 " - " MAN t 7 " " BMA v 3 " - " MAN v 5 " BETA1-4 " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " NAG V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " NAG i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " 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 o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " NAG w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 355 " " NAG A 702 " - " ASN A 234 " " NAG A 703 " - " ASN A 396 " " NAG E 701 " - " ASN E 355 " " NAG E 702 " - " ASN E 234 " " NAG E 703 " - " ASN E 339 " " NAG E 704 " - " ASN E 396 " " NAG I 701 " - " ASN I 355 " " NAG I 702 " - " ASN I 234 " " NAG I 703 " - " ASN I 276 " " NAG I 704 " - " ASN I 339 " " NAG I 705 " - " ASN I 396 " " NAG M 1 " - " ASN E 441 " " NAG N 1 " - " ASN E 301 " " NAG O 1 " - " ASN E 154 " " NAG P 1 " - " ASN E 197 " " NAG Q 1 " - " ASN E 392 " " NAG R 1 " - " ASN E 241 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 158 " " NAG V 1 " - " ASN E 447 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN E 362 " " NAG Z 1 " - " ASN A 441 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 154 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 158 " " NAG h 1 " - " ASN A 262 " " NAG i 1 " - " ASN A 447 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 362 " " NAG l 1 " - " ASN A 276 " " NAG m 1 " - " ASN A 339 " " NAG n 1 " - " ASN I 441 " " NAG o 1 " - " ASN I 301 " " NAG p 1 " - " ASN I 154 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 392 " " NAG s 1 " - " ASN I 241 " " NAG t 1 " - " ASN I 332 " " NAG u 1 " - " ASN I 158 " " NAG v 1 " - " ASN I 262 " " NAG w 1 " - " ASN I 447 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 721.3 milliseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 45 sheets defined 17.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.554A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.035A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 Processing helix chain 'E' and resid 474 through 480 removed outlier: 4.064A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.666A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.626A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.932A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.872A pdb=" N ALA H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.023A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLY A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.941A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.684A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.635A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.733A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.854A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.609A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.108A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.681A pdb=" N SER I 480 " --> pdb=" O ASP I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.969A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.656A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.982A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.611A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.862A pdb=" N ALA L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.337A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.984A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.597A pdb=" N LEU E 260 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 420 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE E 382 " --> pdb=" O LYS E 420 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 466 " --> pdb=" O ASP E 456 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR E 357 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE E 467 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS E 360 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR G 116 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.553A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.497A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.596A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AC3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.816A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 420 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 301 through 302 removed outlier: 4.057A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.779A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.775A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE1, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.954A pdb=" N THR I 202 " --> pdb=" O TYR I 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.006A pdb=" N GLY I 450 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.759A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N LYS K 12 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 698 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6356 1.34 - 1.46: 5312 1.46 - 1.58: 9495 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21340 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.367 -0.036 7.90e-03 1.60e+04 2.04e+01 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 NAG w 3 " pdb=" O5 NAG w 3 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG I 703 " pdb=" O5 NAG I 703 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG i 3 " pdb=" O5 NAG i 3 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 21335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 28259 2.64 - 5.27: 656 5.27 - 7.91: 95 7.91 - 10.54: 13 10.54 - 13.18: 2 Bond angle restraints: 29025 Sorted by residual: angle pdb=" C THR I 257 " pdb=" N GLN I 258 " pdb=" CA GLN I 258 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C ASN I 276 " pdb=" N LEU I 277 " pdb=" CA LEU I 277 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N SER A 388 " pdb=" CA SER A 388 " pdb=" C SER A 388 " ideal model delta sigma weight residual 114.04 109.27 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" CA LEU I 259 " pdb=" CB LEU I 259 " pdb=" CG LEU I 259 " ideal model delta sigma weight residual 116.30 129.48 -13.18 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CB MET I 474 " pdb=" CG MET I 474 " pdb=" SD MET I 474 " ideal model delta sigma weight residual 112.70 123.80 -11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 29020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 10310 16.41 - 32.83: 1033 32.83 - 49.24: 257 49.24 - 65.65: 38 65.65 - 82.07: 17 Dihedral angle restraints: 11655 sinusoidal: 4602 harmonic: 7053 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.29 -58.29 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 444 " pdb=" CB CYS I 444 " ideal model delta sinusoidal sigma weight residual -86.00 -36.15 -49.85 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 11652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3016 0.075 - 0.149: 581 0.149 - 0.224: 58 0.224 - 0.299: 30 0.299 - 0.374: 5 Chirality restraints: 3690 Sorted by residual: chirality pdb=" C1 NAG I 704 " pdb=" ND2 ASN I 339 " pdb=" C2 NAG I 704 " pdb=" O5 NAG I 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 339 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3687 not shown) Planarity restraints: 3542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO E 43 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 176 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO E 177 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 177 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 177 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO L 46 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.025 5.00e-02 4.00e+02 ... (remaining 3539 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3919 2.77 - 3.30: 18111 3.30 - 3.84: 34342 3.84 - 4.37: 38167 4.37 - 4.90: 67764 Nonbonded interactions: 162303 Sorted by model distance: nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.241 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.245 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.248 3.040 nonbonded pdb=" O VAL I 36 " pdb=" OG1 THR J 606 " model vdw 2.253 3.040 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.258 3.040 ... (remaining 162298 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' selection = (chain 'E' and resid 33 through 703) selection = (chain 'I' and resid 33 through 703) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Z' selection = chain 'n' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'b' selection = chain 'h' selection = chain 'p' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'y' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 't' } 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.007 0.053 21524 Z= 0.313 Angle : 0.981 13.178 29538 Z= 0.445 Chirality : 0.063 0.374 3690 Planarity : 0.005 0.050 3492 Dihedral : 13.865 82.067 7020 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2415 helix: -0.46 (0.24), residues: 375 sheet: -0.41 (0.20), residues: 678 loop : -1.38 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 585 TYR 0.017 0.002 TYR K 27 PHE 0.018 0.002 PHE A 376 TRP 0.030 0.002 TRP A 112 HIS 0.007 0.002 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.31 (21340) covalent geometry : angle 0.94098 / 0.44 (29025) SS BOND : bond 0.00409 / 0.28 ( 39) SS BOND : angle 1.19274 / 0.81 ( 78) hydrogen bonds : bond 0.08052 / 5.66 ( 668) hydrogen bonds : angle 6.02119 / 4.37 ( 1851) link_ALPHA1-2 : bond 0.00442 / 0.23 ( 6) link_ALPHA1-2 : angle 2.63971 / 1.54 ( 18) link_ALPHA1-3 : bond 0.00304 / 0.17 ( 9) link_ALPHA1-3 : angle 1.82640 / 1.17 ( 27) link_ALPHA1-6 : bond 0.00460 / 0.29 ( 12) link_ALPHA1-6 : angle 1.53750 / 1.11 ( 36) link_BETA1-4 : bond 0.00733 / 0.46 ( 68) link_BETA1-4 : angle 2.47543 / 1.59 ( 204) link_NAG-ASN : bond 0.00570 / 0.40 ( 50) link_NAG-ASN : angle 2.63075 / 1.94 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8846 (ptm) cc_final: 0.8566 (ptp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1285 time to fit residues: 17.9256 Evaluate side-chains 66 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0970 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 105 HIS E 262 ASN A 258 GLN I 229 ASN I 424 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.056306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041177 restraints weight = 101271.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041943 restraints weight = 71225.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042195 restraints weight = 54289.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042713 restraints weight = 52412.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042728 restraints weight = 47346.618| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21524 Z= 0.135 Angle : 0.589 11.145 29538 Z= 0.283 Chirality : 0.043 0.231 3690 Planarity : 0.004 0.038 3492 Dihedral : 4.591 19.152 2637 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.24 % Allowed : 5.19 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2415 helix: 0.93 (0.28), residues: 375 sheet: -0.50 (0.19), residues: 729 loop : -1.11 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.012 0.001 TYR D 51 PHE 0.010 0.001 PHE I 383 TRP 0.017 0.001 TRP A 112 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21340) covalent geometry : angle 0.55269 / 0.28 (29025) SS BOND : bond 0.00163 / 0.11 ( 39) SS BOND : angle 0.64912 / 0.42 ( 78) hydrogen bonds : bond 0.03521 / 2.42 ( 668) hydrogen bonds : angle 5.08839 / 3.65 ( 1851) link_ALPHA1-2 : bond 0.00398 / 0.20 ( 6) link_ALPHA1-2 : angle 1.97642 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00561 / 0.31 ( 9) link_ALPHA1-3 : angle 1.55906 / 0.99 ( 27) link_ALPHA1-6 : bond 0.00550 / 0.35 ( 12) link_ALPHA1-6 : angle 1.43578 / 0.98 ( 36) link_BETA1-4 : bond 0.00460 / 0.30 ( 68) link_BETA1-4 : angle 1.68119 / 1.09 ( 204) link_NAG-ASN : bond 0.00277 / 0.20 ( 50) link_NAG-ASN : angle 1.92250 / 1.42 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8789 (ptm) cc_final: 0.8516 (ptm) REVERT: I 433 MET cc_start: 0.8764 (ttm) cc_final: 0.8452 (ttm) REVERT: K 70 MET cc_start: 0.7898 (mmm) cc_final: 0.6340 (mmt) REVERT: K 76 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8655 (tt) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.1239 time to fit residues: 14.8680 Evaluate side-chains 69 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 658 GLN A 421 GLN B 653 GLN D 16 GLN I 105 HIS J 540 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.054922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039221 restraints weight = 105048.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040611 restraints weight = 74687.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040548 restraints weight = 56655.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040697 restraints weight = 58490.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040779 restraints weight = 52748.858| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21524 Z= 0.315 Angle : 0.746 7.549 29538 Z= 0.360 Chirality : 0.048 0.241 3690 Planarity : 0.004 0.046 3492 Dihedral : 5.031 22.715 2637 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.66 % Allowed : 9.90 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2415 helix: 0.85 (0.29), residues: 375 sheet: -0.43 (0.19), residues: 705 loop : -1.31 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 579 TYR 0.019 0.002 TYR E 223 PHE 0.023 0.002 PHE A 376 TRP 0.019 0.002 TRP A 112 HIS 0.014 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.32 (21340) covalent geometry : angle 0.71063 / 0.35 (29025) SS BOND : bond 0.00335 / 0.23 ( 39) SS BOND : angle 1.17122 / 0.79 ( 78) hydrogen bonds : bond 0.04586 / 3.13 ( 668) hydrogen bonds : angle 5.47507 / 3.92 ( 1851) link_ALPHA1-2 : bond 0.00414 / 0.24 ( 6) link_ALPHA1-2 : angle 2.02238 / 1.22 ( 18) link_ALPHA1-3 : bond 0.00252 / 0.14 ( 9) link_ALPHA1-3 : angle 1.65550 / 1.09 ( 27) link_ALPHA1-6 : bond 0.00450 / 0.29 ( 12) link_ALPHA1-6 : angle 1.49666 / 1.04 ( 36) link_BETA1-4 : bond 0.00512 / 0.33 ( 68) link_BETA1-4 : angle 1.75487 / 1.15 ( 204) link_NAG-ASN : bond 0.00509 / 0.34 ( 50) link_NAG-ASN : angle 2.30792 / 1.66 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: E 152 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8674 (mtm) REVERT: C 70 MET cc_start: 0.8784 (mtt) cc_final: 0.8093 (mtt) REVERT: K 70 MET cc_start: 0.8378 (mmm) cc_final: 0.6551 (mmt) outliers start: 14 outliers final: 4 residues processed: 76 average time/residue: 0.1235 time to fit residues: 16.4743 Evaluate side-chains 68 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain I residue 374 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 230 optimal weight: 30.0000 chunk 213 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN D 16 GLN I 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.056182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041141 restraints weight = 101076.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042090 restraints weight = 69608.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.042283 restraints weight = 53443.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042611 restraints weight = 51830.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042660 restraints weight = 47552.080| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21524 Z= 0.098 Angle : 0.551 7.527 29538 Z= 0.264 Chirality : 0.041 0.251 3690 Planarity : 0.003 0.037 3492 Dihedral : 4.418 19.919 2637 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.57 % Allowed : 10.75 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2415 helix: 1.54 (0.29), residues: 372 sheet: -0.41 (0.19), residues: 735 loop : -1.01 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR D 51 PHE 0.009 0.001 PHE I 383 TRP 0.018 0.001 TRP A 112 HIS 0.002 0.001 HIS E 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (21340) covalent geometry : angle 0.52034 / 0.26 (29025) SS BOND : bond 0.00170 / 0.11 ( 39) SS BOND : angle 0.47723 / 0.32 ( 78) hydrogen bonds : bond 0.03316 / 2.28 ( 668) hydrogen bonds : angle 4.89344 / 3.48 ( 1851) link_ALPHA1-2 : bond 0.00335 / 0.16 ( 6) link_ALPHA1-2 : angle 1.72615 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00496 / 0.28 ( 9) link_ALPHA1-3 : angle 1.44632 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00558 / 0.35 ( 12) link_ALPHA1-6 : angle 1.36105 / 0.94 ( 36) link_BETA1-4 : bond 0.00419 / 0.27 ( 68) link_BETA1-4 : angle 1.52165 / 0.97 ( 204) link_NAG-ASN : bond 0.00291 / 0.21 ( 50) link_NAG-ASN : angle 1.72521 / 1.25 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8718 (tt) REVERT: G 70 MET cc_start: 0.8559 (mtt) cc_final: 0.7735 (mtt) REVERT: C 70 MET cc_start: 0.8802 (mtt) cc_final: 0.8116 (mtt) REVERT: I 259 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9022 (mp) REVERT: K 70 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6289 (mmt) outliers start: 12 outliers final: 7 residues processed: 78 average time/residue: 0.1199 time to fit residues: 15.9628 Evaluate side-chains 76 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 96 optimal weight: 0.1980 chunk 230 optimal weight: 30.0000 chunk 209 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040832 restraints weight = 102931.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041548 restraints weight = 72182.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041644 restraints weight = 55502.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041905 restraints weight = 53846.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041940 restraints weight = 50480.346| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21524 Z= 0.125 Angle : 0.551 6.950 29538 Z= 0.263 Chirality : 0.042 0.215 3690 Planarity : 0.003 0.036 3492 Dihedral : 4.294 19.375 2637 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.80 % Allowed : 11.93 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2415 helix: 1.71 (0.29), residues: 375 sheet: -0.34 (0.19), residues: 708 loop : -0.95 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 585 TYR 0.012 0.001 TYR H 51 PHE 0.008 0.001 PHE A 317 TRP 0.013 0.001 TRP A 112 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (21340) covalent geometry : angle 0.52158 / 0.26 (29025) SS BOND : bond 0.00213 / 0.15 ( 39) SS BOND : angle 0.60359 / 0.41 ( 78) hydrogen bonds : bond 0.03307 / 2.26 ( 668) hydrogen bonds : angle 4.83960 / 3.45 ( 1851) link_ALPHA1-2 : bond 0.00297 / 0.14 ( 6) link_ALPHA1-2 : angle 1.75124 / 1.07 ( 18) link_ALPHA1-3 : bond 0.00426 / 0.24 ( 9) link_ALPHA1-3 : angle 1.50310 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00476 / 0.30 ( 12) link_ALPHA1-6 : angle 1.39939 / 0.97 ( 36) link_BETA1-4 : bond 0.00429 / 0.28 ( 68) link_BETA1-4 : angle 1.47008 / 0.94 ( 204) link_NAG-ASN : bond 0.00274 / 0.20 ( 50) link_NAG-ASN : angle 1.65695 / 1.21 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8707 (tt) REVERT: G 70 MET cc_start: 0.8604 (mtt) cc_final: 0.7739 (mtt) REVERT: C 70 MET cc_start: 0.8746 (mtt) cc_final: 0.8147 (mtt) REVERT: I 259 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9056 (mp) REVERT: K 70 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7196 (mmm) outliers start: 17 outliers final: 5 residues processed: 78 average time/residue: 0.1199 time to fit residues: 16.7464 Evaluate side-chains 74 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 231 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 187 ASN E 258 GLN F 653 GLN B 650 GLN B 653 GLN D 16 GLN I 187 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.055261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040191 restraints weight = 104564.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040623 restraints weight = 78326.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040761 restraints weight = 62163.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.040988 restraints weight = 60119.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.041026 restraints weight = 56890.828| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21524 Z= 0.265 Angle : 0.675 6.990 29538 Z= 0.323 Chirality : 0.046 0.223 3690 Planarity : 0.004 0.037 3492 Dihedral : 4.711 20.044 2637 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.32 % Allowed : 12.78 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2415 helix: 1.31 (0.29), residues: 375 sheet: -0.41 (0.19), residues: 708 loop : -1.11 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.015 0.002 TYR E 223 PHE 0.013 0.002 PHE I 53 TRP 0.014 0.002 TRP I 69 HIS 0.009 0.002 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 (21340) covalent geometry : angle 0.64460 / 0.32 (29025) SS BOND : bond 0.00322 / 0.23 ( 39) SS BOND : angle 0.95675 / 0.64 ( 78) hydrogen bonds : bond 0.04164 / 2.84 ( 668) hydrogen bonds : angle 5.22193 / 3.73 ( 1851) link_ALPHA1-2 : bond 0.00485 / 0.27 ( 6) link_ALPHA1-2 : angle 1.93232 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00212 / 0.11 ( 9) link_ALPHA1-3 : angle 1.56568 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00404 / 0.26 ( 12) link_ALPHA1-6 : angle 1.46622 / 1.02 ( 36) link_BETA1-4 : bond 0.00452 / 0.29 ( 68) link_BETA1-4 : angle 1.60288 / 1.04 ( 204) link_NAG-ASN : bond 0.00437 / 0.30 ( 50) link_NAG-ASN : angle 1.99775 / 1.43 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8826 (tt) REVERT: G 70 MET cc_start: 0.8712 (mtt) cc_final: 0.7800 (mtt) REVERT: A 125 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 70 MET cc_start: 0.8886 (mtt) cc_final: 0.8222 (mtt) REVERT: I 259 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9126 (mp) REVERT: K 70 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7717 (mmm) outliers start: 28 outliers final: 14 residues processed: 84 average time/residue: 0.1068 time to fit residues: 16.1830 Evaluate side-chains 80 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 146 optimal weight: 0.0170 chunk 131 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 187 ASN F 653 GLN B 653 GLN I 187 ASN I 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.056032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041127 restraints weight = 104583.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041432 restraints weight = 79011.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041782 restraints weight = 61801.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041940 restraints weight = 57795.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.042006 restraints weight = 53846.962| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21524 Z= 0.100 Angle : 0.548 8.019 29538 Z= 0.261 Chirality : 0.041 0.236 3690 Planarity : 0.003 0.036 3492 Dihedral : 4.328 20.670 2637 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.08 % Allowed : 13.44 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.17), residues: 2415 helix: 1.73 (0.29), residues: 375 sheet: -0.31 (0.19), residues: 708 loop : -0.90 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR H 51 PHE 0.008 0.001 PHE E 53 TRP 0.017 0.001 TRP A 112 HIS 0.009 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (21340) covalent geometry : angle 0.51915 / 0.25 (29025) SS BOND : bond 0.00212 / 0.15 ( 39) SS BOND : angle 0.54490 / 0.36 ( 78) hydrogen bonds : bond 0.03282 / 2.25 ( 668) hydrogen bonds : angle 4.82962 / 3.43 ( 1851) link_ALPHA1-2 : bond 0.00263 / 0.12 ( 6) link_ALPHA1-2 : angle 1.72148 / 1.08 ( 18) link_ALPHA1-3 : bond 0.00480 / 0.27 ( 9) link_ALPHA1-3 : angle 1.46842 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00519 / 0.33 ( 12) link_ALPHA1-6 : angle 1.37492 / 0.96 ( 36) link_BETA1-4 : bond 0.00417 / 0.27 ( 68) link_BETA1-4 : angle 1.47191 / 0.94 ( 204) link_NAG-ASN : bond 0.00255 / 0.19 ( 50) link_NAG-ASN : angle 1.62831 / 1.17 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8701 (tt) REVERT: G 70 MET cc_start: 0.8650 (mtt) cc_final: 0.7732 (mtt) REVERT: C 70 MET cc_start: 0.8839 (mtt) cc_final: 0.8222 (mtt) REVERT: I 44 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8175 (t) REVERT: I 259 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9083 (mp) outliers start: 23 outliers final: 10 residues processed: 84 average time/residue: 0.1137 time to fit residues: 16.7105 Evaluate side-chains 78 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 374 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.055886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040844 restraints weight = 104221.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041531 restraints weight = 73539.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041597 restraints weight = 57988.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041835 restraints weight = 56711.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041864 restraints weight = 53458.229| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21524 Z= 0.127 Angle : 0.555 7.672 29538 Z= 0.263 Chirality : 0.042 0.219 3690 Planarity : 0.003 0.035 3492 Dihedral : 4.279 20.240 2637 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.85 % Allowed : 13.91 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2415 helix: 1.81 (0.29), residues: 375 sheet: -0.28 (0.19), residues: 708 loop : -0.87 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR H 51 PHE 0.012 0.001 PHE I 383 TRP 0.014 0.001 TRP A 112 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21340) covalent geometry : angle 0.52739 / 0.26 (29025) SS BOND : bond 0.00227 / 0.16 ( 39) SS BOND : angle 0.59085 / 0.39 ( 78) hydrogen bonds : bond 0.03302 / 2.26 ( 668) hydrogen bonds : angle 4.78920 / 3.41 ( 1851) link_ALPHA1-2 : bond 0.00266 / 0.13 ( 6) link_ALPHA1-2 : angle 1.72732 / 1.06 ( 18) link_ALPHA1-3 : bond 0.00425 / 0.24 ( 9) link_ALPHA1-3 : angle 1.48743 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00480 / 0.30 ( 12) link_ALPHA1-6 : angle 1.39698 / 0.97 ( 36) link_BETA1-4 : bond 0.00423 / 0.27 ( 68) link_BETA1-4 : angle 1.45154 / 0.93 ( 204) link_NAG-ASN : bond 0.00252 / 0.18 ( 50) link_NAG-ASN : angle 1.60990 / 1.17 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8678 (tt) REVERT: G 70 MET cc_start: 0.8650 (mtt) cc_final: 0.7721 (mtt) REVERT: C 70 MET cc_start: 0.8844 (mtt) cc_final: 0.8088 (mtt) REVERT: I 44 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8187 (t) REVERT: I 259 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9069 (mp) REVERT: K 70 MET cc_start: 0.8530 (mmm) cc_final: 0.6562 (mmt) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.1102 time to fit residues: 15.7887 Evaluate side-chains 80 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 0.2980 chunk 73 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 237 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041454 restraints weight = 104161.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041769 restraints weight = 79322.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042120 restraints weight = 61894.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.042483 restraints weight = 57635.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.042489 restraints weight = 53370.980| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21524 Z= 0.092 Angle : 0.531 7.898 29538 Z= 0.252 Chirality : 0.041 0.214 3690 Planarity : 0.003 0.034 3492 Dihedral : 4.151 19.890 2637 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.80 % Allowed : 14.10 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2415 helix: 1.89 (0.28), residues: 378 sheet: -0.23 (0.19), residues: 714 loop : -0.77 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.012 0.001 TYR H 51 PHE 0.012 0.001 PHE I 383 TRP 0.015 0.001 TRP A 112 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (21340) covalent geometry : angle 0.50368 / 0.25 (29025) SS BOND : bond 0.00193 / 0.13 ( 39) SS BOND : angle 0.53028 / 0.36 ( 78) hydrogen bonds : bond 0.03077 / 2.10 ( 668) hydrogen bonds : angle 4.65515 / 3.31 ( 1851) link_ALPHA1-2 : bond 0.00271 / 0.12 ( 6) link_ALPHA1-2 : angle 1.69930 / 1.05 ( 18) link_ALPHA1-3 : bond 0.00502 / 0.28 ( 9) link_ALPHA1-3 : angle 1.48757 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00516 / 0.32 ( 12) link_ALPHA1-6 : angle 1.37702 / 0.96 ( 36) link_BETA1-4 : bond 0.00418 / 0.27 ( 68) link_BETA1-4 : angle 1.43372 / 0.91 ( 204) link_NAG-ASN : bond 0.00232 / 0.17 ( 50) link_NAG-ASN : angle 1.50434 / 1.10 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8713 (tt) REVERT: G 70 MET cc_start: 0.8638 (mtt) cc_final: 0.7690 (mtt) REVERT: C 70 MET cc_start: 0.8822 (mtt) cc_final: 0.8089 (mtt) REVERT: I 44 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8148 (t) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1103 time to fit residues: 15.2831 Evaluate side-chains 80 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN I 374 HIS L 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.055349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040346 restraints weight = 105363.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040725 restraints weight = 75691.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.040894 restraints weight = 62103.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041088 restraints weight = 60493.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.041116 restraints weight = 56754.426| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21524 Z= 0.270 Angle : 0.674 12.217 29538 Z= 0.321 Chirality : 0.046 0.207 3690 Planarity : 0.004 0.035 3492 Dihedral : 4.586 20.144 2637 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.85 % Allowed : 14.33 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2415 helix: 1.49 (0.29), residues: 378 sheet: -0.34 (0.19), residues: 714 loop : -0.99 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 579 TYR 0.015 0.002 TYR E 223 PHE 0.015 0.002 PHE I 383 TRP 0.014 0.002 TRP E 96 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (21340) covalent geometry : angle 0.64535 / 0.32 (29025) SS BOND : bond 0.00341 / 0.24 ( 39) SS BOND : angle 0.96224 / 0.63 ( 78) hydrogen bonds : bond 0.04042 / 2.76 ( 668) hydrogen bonds : angle 5.10048 / 3.64 ( 1851) link_ALPHA1-2 : bond 0.00463 / 0.27 ( 6) link_ALPHA1-2 : angle 1.91427 / 1.16 ( 18) link_ALPHA1-3 : bond 0.00211 / 0.12 ( 9) link_ALPHA1-3 : angle 1.57371 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00392 / 0.25 ( 12) link_ALPHA1-6 : angle 1.47744 / 1.03 ( 36) link_BETA1-4 : bond 0.00447 / 0.29 ( 68) link_BETA1-4 : angle 1.56831 / 1.02 ( 204) link_NAG-ASN : bond 0.00447 / 0.30 ( 50) link_NAG-ASN : angle 1.89039 / 1.34 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8823 (tt) REVERT: G 70 MET cc_start: 0.8695 (mtt) cc_final: 0.7762 (mtt) REVERT: C 70 MET cc_start: 0.8881 (mtt) cc_final: 0.8115 (mtt) REVERT: I 433 MET cc_start: 0.8767 (ttm) cc_final: 0.8508 (ttm) REVERT: K 70 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7295 (mmm) outliers start: 18 outliers final: 14 residues processed: 79 average time/residue: 0.1157 time to fit residues: 16.3306 Evaluate side-chains 80 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN I 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.055901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041149 restraints weight = 104303.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041560 restraints weight = 74668.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041750 restraints weight = 60131.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041902 restraints weight = 57472.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041963 restraints weight = 54682.240| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21524 Z= 0.110 Angle : 0.565 12.239 29538 Z= 0.267 Chirality : 0.042 0.222 3690 Planarity : 0.003 0.035 3492 Dihedral : 4.345 20.777 2637 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.90 % Allowed : 14.47 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2415 helix: 1.79 (0.29), residues: 375 sheet: -0.26 (0.20), residues: 708 loop : -0.83 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR D 51 PHE 0.013 0.001 PHE I 383 TRP 0.018 0.001 TRP A 112 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21340) covalent geometry : angle 0.53811 / 0.26 (29025) SS BOND : bond 0.00203 / 0.14 ( 39) SS BOND : angle 0.55840 / 0.38 ( 78) hydrogen bonds : bond 0.03341 / 2.29 ( 668) hydrogen bonds : angle 4.77853 / 3.40 ( 1851) link_ALPHA1-2 : bond 0.00249 / 0.11 ( 6) link_ALPHA1-2 : angle 1.73231 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00485 / 0.27 ( 9) link_ALPHA1-3 : angle 1.48991 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00524 / 0.33 ( 12) link_ALPHA1-6 : angle 1.39266 / 0.98 ( 36) link_BETA1-4 : bond 0.00414 / 0.27 ( 68) link_BETA1-4 : angle 1.47418 / 0.94 ( 204) link_NAG-ASN : bond 0.00231 / 0.17 ( 50) link_NAG-ASN : angle 1.60677 / 1.14 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2646.56 seconds wall clock time: 47 minutes 12.64 seconds (2832.64 seconds total)