Starting phenix.real_space_refine on Sun Aug 24 15:46:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.map" model { file = "/net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dy6_27776/08_2025/8dy6_27776.cif" } resolution = 4.32 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= 0.006 sd= 0.128 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 12918 2.51 5 N 3363 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20778 Number of models: 1 Model: "" Number of chains: 54 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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 dihedrals: 15 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.71, per 1000 atoms: 0.18 Number of scatterers: 20778 At special positions: 0 Unit cell: (159.84, 156.6, 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 4365 8.00 N 3363 7.00 C 12918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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 433 " distance=2.02 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 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.02 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 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 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 433 " 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 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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=2.04 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 U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA U 3 " - " MAN U 7 " " BMA W 3 " - " MAN W 5 " " BMA g 3 " - " MAN g 7 " " BMA i 3 " - " MAN i 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " NAG X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " NAG j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG 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 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 396 " " NAG A 703 " - " ASN A 234 " " 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 M 1 " - " ASN A 154 " " NAG N 1 " - " ASN E 154 " " NAG O 1 " - " ASN I 154 " " NAG P 1 " - " ASN E 442 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 392 " " NAG T 1 " - " ASN E 241 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 158 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 362 " " NAG b 1 " - " ASN A 442 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 392 " " NAG f 1 " - " ASN A 241 " " NAG g 1 " - " ASN A 332 " " NAG h 1 " - " ASN A 158 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN A 386 " " NAG l 1 " - " ASN A 362 " " NAG m 1 " - " ASN A 276 " " NAG n 1 " - " ASN A 339 " " NAG o 1 " - " ASN I 442 " " NAG p 1 " - " ASN I 301 " " 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 w 1 " - " ASN I 448 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 644.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 49 helices and 33 sheets defined 19.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.565A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.686A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.246A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.942A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.865A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.037A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.790A pdb=" N GLN C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.689A pdb=" N ALA D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 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 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.564A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 543 removed outlier: 3.630A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 4.135A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.126A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.830A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.509A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.589A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.632A 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 475 through 480 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 542 removed outlier: 4.222A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 597 removed outlier: 4.292A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.788A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.608A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.748A pdb=" N GLN K 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.561A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.789A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.855A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.800A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 12 current: chain 'D' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 46 through 50 current: chain 'D' and resid 98 through 101 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.267A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.653A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.764A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.921A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 12 current: chain 'H' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 47 through 50 current: chain 'H' and resid 99 through 101 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'I' and resid 494 through 498 removed outlier: 5.268A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.601A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.519A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AD1, first strand: chain 'I' and resid 201 through 203 removed outlier: 3.525A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 6.909A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 413 through 420 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 58 through 60 current: chain 'K' and resid 116 through 117 Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 50 current: chain 'L' and resid 98 through 101 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 18 through 23 517 hydrogen bonds defined for protein. 1416 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: 2.52 Time building geometry restraints manager: 2.42 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: 6275 1.34 - 1.46: 5236 1.46 - 1.58: 9510 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21198 Sorted by residual: bond pdb=" C3 BMA O 3 " pdb=" O3 BMA O 3 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.72e+00 bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" C1 MAN U 4 " pdb=" O5 MAN U 4 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 21193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 27685 2.25 - 4.49: 972 4.49 - 6.74: 129 6.74 - 8.98: 42 8.98 - 11.23: 5 Bond angle restraints: 28833 Sorted by residual: angle pdb=" N ILE J 635 " pdb=" CA ILE J 635 " pdb=" C ILE J 635 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.02e+01 angle pdb=" N ILE F 635 " pdb=" CA ILE F 635 " pdb=" C ILE F 635 " ideal model delta sigma weight residual 112.29 108.20 4.09 9.40e-01 1.13e+00 1.89e+01 angle pdb=" C TRP C 47 " pdb=" N MET C 48 " pdb=" CA MET C 48 " ideal model delta sigma weight residual 122.08 115.55 6.53 1.53e+00 4.27e-01 1.82e+01 angle pdb=" C LEU I 261 " pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASN E 276 " pdb=" N LEU E 277 " pdb=" CA LEU E 277 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 28828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 13167 22.16 - 44.31: 778 44.31 - 66.47: 147 66.47 - 88.63: 165 88.63 - 110.78: 92 Dihedral angle restraints: 14349 sinusoidal: 7293 harmonic: 7056 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 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+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 93.00 157.13 -64.13 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.42 -60.42 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 14346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2991 0.076 - 0.151: 551 0.151 - 0.227: 49 0.227 - 0.302: 22 0.302 - 0.378: 6 Chirality restraints: 3619 Sorted by residual: chirality pdb=" C1 NAG E 702 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 702 " pdb=" O5 NAG E 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C5 BMA v 3 " pdb=" C4 BMA v 3 " pdb=" C6 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 3616 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 653 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C GLN F 653 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN F 653 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 654 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 646 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C LEU F 646 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU F 646 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU F 647 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 652 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C GLN F 652 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN F 652 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN F 653 " -0.014 2.00e-02 2.50e+03 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5210 2.79 - 3.32: 19098 3.32 - 3.85: 35670 3.85 - 4.37: 39146 4.37 - 4.90: 67020 Nonbonded interactions: 166144 Sorted by model distance: nonbonded pdb=" O ALA D 94 " pdb=" OG1 THR D 98 " model vdw 2.266 3.040 nonbonded pdb=" O ILE I 358 " pdb=" OG1 THR I 394 " model vdw 2.272 3.040 nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.282 3.040 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.282 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.284 3.040 ... (remaining 166139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 702) selection = (chain 'E' and resid 33 through 702) selection = chain 'I' } 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' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' 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 'S' selection = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'l' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'U' selection = chain 'g' selection = chain 't' } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'v' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.860 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.006 0.075 21367 Z= 0.312 Angle : 1.016 15.068 29301 Z= 0.492 Chirality : 0.061 0.378 3619 Planarity : 0.006 0.048 3492 Dihedral : 19.225 110.784 9714 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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 aren not related in a simple way. whole: -1.13 (0.16), residues: 2415 helix: -0.65 (0.24), residues: 408 sheet: -0.17 (0.20), residues: 636 loop : -1.04 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 585 TYR 0.029 0.002 TYR A 217 PHE 0.016 0.002 PHE I 53 TRP 0.032 0.003 TRP C 36 HIS 0.005 0.002 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00640 (21198) covalent geometry : angle 0.97160 (28833) SS BOND : bond 0.00427 ( 39) SS BOND : angle 1.03704 ( 78) hydrogen bonds : bond 0.14143 ( 517) hydrogen bonds : angle 6.28534 ( 1416) link_ALPHA1-2 : bond 0.00574 ( 6) link_ALPHA1-2 : angle 2.95635 ( 18) link_ALPHA1-3 : bond 0.00581 ( 7) link_ALPHA1-3 : angle 2.34741 ( 21) link_ALPHA1-6 : bond 0.00099 ( 6) link_ALPHA1-6 : angle 1.85314 ( 18) link_BETA1-4 : bond 0.00760 ( 65) link_BETA1-4 : angle 2.30257 ( 195) link_NAG-ASN : bond 0.00695 ( 46) link_NAG-ASN : angle 3.38701 ( 138) *********************** 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 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.534 Fit side-chains REVERT: C 81 MET cc_start: 0.8905 (mmp) cc_final: 0.8612 (mmp) REVERT: E 104 MET cc_start: 0.9262 (tpp) cc_final: 0.8634 (tpp) REVERT: G 70 MET cc_start: 0.8330 (mpp) cc_final: 0.7959 (mpp) REVERT: I 104 MET cc_start: 0.9067 (tmm) cc_final: 0.8795 (tmm) REVERT: K 70 MET cc_start: 0.7839 (mtm) cc_final: 0.7553 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1190 time to fit residues: 10.2261 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 20.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 577 GLN B 630 GLN B 651 ASN E 229 ASN E 428 GLN F 651 ASN I 350 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.023791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.018347 restraints weight = 331886.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.018857 restraints weight = 201905.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.019187 restraints weight = 149234.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.019404 restraints weight = 123877.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.019544 restraints weight = 110248.818| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21367 Z= 0.248 Angle : 0.739 9.630 29301 Z= 0.344 Chirality : 0.046 0.269 3619 Planarity : 0.004 0.037 3492 Dihedral : 14.787 81.672 5328 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.75 % 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 aren not related in a simple way. whole: -0.50 (0.17), residues: 2415 helix: 0.71 (0.27), residues: 396 sheet: -0.18 (0.20), residues: 636 loop : -0.68 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.021 0.002 TYR L 51 PHE 0.016 0.002 PHE I 382 TRP 0.024 0.002 TRP G 36 HIS 0.005 0.002 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00526 (21198) covalent geometry : angle 0.68916 (28833) SS BOND : bond 0.00288 ( 39) SS BOND : angle 0.79702 ( 78) hydrogen bonds : bond 0.04506 ( 517) hydrogen bonds : angle 5.43581 ( 1416) link_ALPHA1-2 : bond 0.00551 ( 6) link_ALPHA1-2 : angle 2.29213 ( 18) link_ALPHA1-3 : bond 0.00879 ( 7) link_ALPHA1-3 : angle 2.44083 ( 21) link_ALPHA1-6 : bond 0.00307 ( 6) link_ALPHA1-6 : angle 2.05016 ( 18) link_BETA1-4 : bond 0.00531 ( 65) link_BETA1-4 : angle 2.32895 ( 195) link_NAG-ASN : bond 0.00656 ( 46) link_NAG-ASN : angle 2.57520 ( 138) *********************** 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 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: I 104 MET cc_start: 0.9231 (tmm) cc_final: 0.8823 (tmm) REVERT: I 350 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: K 70 MET cc_start: 0.8230 (mtm) cc_final: 0.7867 (mtp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1031 time to fit residues: 8.6297 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN E 103 GLN F 651 ASN H 39 GLN J 577 GLN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.023746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.018247 restraints weight = 331145.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.018749 restraints weight = 202066.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.019081 restraints weight = 149529.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.019295 restraints weight = 124470.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.019430 restraints weight = 110866.237| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21367 Z= 0.232 Angle : 0.705 8.991 29301 Z= 0.329 Chirality : 0.046 0.282 3619 Planarity : 0.004 0.036 3492 Dihedral : 12.059 83.158 5328 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % 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 aren not related in a simple way. whole: -0.41 (0.18), residues: 2415 helix: 1.00 (0.28), residues: 402 sheet: -0.34 (0.20), residues: 657 loop : -0.57 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.045 0.002 TYR L 51 PHE 0.019 0.002 PHE I 382 TRP 0.016 0.002 TRP B 628 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00494 (21198) covalent geometry : angle 0.66014 (28833) SS BOND : bond 0.00312 ( 39) SS BOND : angle 0.72069 ( 78) hydrogen bonds : bond 0.04260 ( 517) hydrogen bonds : angle 5.33781 ( 1416) link_ALPHA1-2 : bond 0.00546 ( 6) link_ALPHA1-2 : angle 2.29754 ( 18) link_ALPHA1-3 : bond 0.00950 ( 7) link_ALPHA1-3 : angle 2.27615 ( 21) link_ALPHA1-6 : bond 0.00318 ( 6) link_ALPHA1-6 : angle 2.01450 ( 18) link_BETA1-4 : bond 0.00532 ( 65) link_BETA1-4 : angle 2.06479 ( 195) link_NAG-ASN : bond 0.00546 ( 46) link_NAG-ASN : angle 2.45328 ( 138) *********************** 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 48 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9297 (tmm) cc_final: 0.8936 (tmm) REVERT: E 104 MET cc_start: 0.9321 (tpp) cc_final: 0.8686 (tpp) REVERT: E 434 MET cc_start: 0.8830 (ttm) cc_final: 0.8458 (ttp) REVERT: K 70 MET cc_start: 0.8033 (mtm) cc_final: 0.7707 (mtp) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.1351 time to fit residues: 11.7225 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 191 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 151 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 119 optimal weight: 0.0470 overall best weight: 6.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.023711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.018197 restraints weight = 331825.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.018693 restraints weight = 204534.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.019018 restraints weight = 152077.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.019228 restraints weight = 126910.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.019363 restraints weight = 113435.793| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21367 Z= 0.250 Angle : 0.712 9.098 29301 Z= 0.334 Chirality : 0.046 0.278 3619 Planarity : 0.004 0.037 3492 Dihedral : 10.841 84.593 5328 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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 aren not related in a simple way. whole: -0.50 (0.18), residues: 2415 helix: 1.06 (0.28), residues: 402 sheet: -0.58 (0.19), residues: 681 loop : -0.57 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 585 TYR 0.032 0.002 TYR L 51 PHE 0.017 0.002 PHE I 382 TRP 0.024 0.002 TRP J 614 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00534 (21198) covalent geometry : angle 0.66860 (28833) SS BOND : bond 0.00393 ( 39) SS BOND : angle 0.71469 ( 78) hydrogen bonds : bond 0.04235 ( 517) hydrogen bonds : angle 5.36304 ( 1416) link_ALPHA1-2 : bond 0.00655 ( 6) link_ALPHA1-2 : angle 2.27091 ( 18) link_ALPHA1-3 : bond 0.00907 ( 7) link_ALPHA1-3 : angle 2.34105 ( 21) link_ALPHA1-6 : bond 0.00431 ( 6) link_ALPHA1-6 : angle 2.11593 ( 18) link_BETA1-4 : bond 0.00551 ( 65) link_BETA1-4 : angle 2.05530 ( 195) link_NAG-ASN : bond 0.00607 ( 46) link_NAG-ASN : angle 2.45670 ( 138) *********************** 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 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.827 Fit side-chains REVERT: I 104 MET cc_start: 0.9255 (tmm) cc_final: 0.9047 (tmm) REVERT: I 434 MET cc_start: 0.8806 (mmm) cc_final: 0.8441 (ttm) REVERT: K 70 MET cc_start: 0.8323 (mtm) cc_final: 0.7670 (mtp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1384 time to fit residues: 11.4467 Evaluate side-chains 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 189 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 141 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN H 39 GLN I 425 ASN J 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.023837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.018299 restraints weight = 329622.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.018798 restraints weight = 203547.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.019131 restraints weight = 151643.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.019342 restraints weight = 126456.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.019480 restraints weight = 113004.297| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21367 Z= 0.212 Angle : 0.670 10.849 29301 Z= 0.315 Chirality : 0.045 0.273 3619 Planarity : 0.003 0.036 3492 Dihedral : 10.191 86.027 5328 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 aren not related in a simple way. whole: -0.43 (0.18), residues: 2415 helix: 1.20 (0.28), residues: 402 sheet: -0.59 (0.20), residues: 672 loop : -0.51 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 503 TYR 0.027 0.002 TYR L 51 PHE 0.016 0.002 PHE I 382 TRP 0.021 0.002 TRP J 614 HIS 0.004 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00454 (21198) covalent geometry : angle 0.62757 (28833) SS BOND : bond 0.00283 ( 39) SS BOND : angle 0.73763 ( 78) hydrogen bonds : bond 0.04090 ( 517) hydrogen bonds : angle 5.25852 ( 1416) link_ALPHA1-2 : bond 0.00587 ( 6) link_ALPHA1-2 : angle 2.15581 ( 18) link_ALPHA1-3 : bond 0.00984 ( 7) link_ALPHA1-3 : angle 2.12910 ( 21) link_ALPHA1-6 : bond 0.00541 ( 6) link_ALPHA1-6 : angle 1.99958 ( 18) link_BETA1-4 : bond 0.00506 ( 65) link_BETA1-4 : angle 1.85782 ( 195) link_NAG-ASN : bond 0.00505 ( 46) link_NAG-ASN : angle 2.47154 ( 138) *********************** 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 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.923 Fit side-chains REVERT: A 104 MET cc_start: 0.9364 (tmm) cc_final: 0.8729 (tmm) REVERT: E 104 MET cc_start: 0.9258 (tpp) cc_final: 0.8848 (tpp) REVERT: I 104 MET cc_start: 0.9234 (tmm) cc_final: 0.8626 (tmm) REVERT: K 70 MET cc_start: 0.8000 (mtm) cc_final: 0.7615 (mtp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1350 time to fit residues: 10.8971 Evaluate side-chains 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 77 optimal weight: 40.0000 chunk 202 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.023789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.018281 restraints weight = 327702.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.018776 restraints weight = 202346.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.019097 restraints weight = 151359.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.019311 restraints weight = 126530.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.019435 restraints weight = 112859.837| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21367 Z= 0.228 Angle : 0.687 9.769 29301 Z= 0.322 Chirality : 0.045 0.269 3619 Planarity : 0.003 0.036 3492 Dihedral : 9.751 87.486 5328 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 aren not related in a simple way. whole: -0.46 (0.18), residues: 2415 helix: 1.18 (0.28), residues: 402 sheet: -0.66 (0.20), residues: 672 loop : -0.51 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 503 TYR 0.036 0.002 TYR L 51 PHE 0.016 0.002 PHE I 382 TRP 0.022 0.002 TRP B 614 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00487 (21198) covalent geometry : angle 0.64499 (28833) SS BOND : bond 0.00321 ( 39) SS BOND : angle 0.78747 ( 78) hydrogen bonds : bond 0.04059 ( 517) hydrogen bonds : angle 5.33915 ( 1416) link_ALPHA1-2 : bond 0.00711 ( 6) link_ALPHA1-2 : angle 2.19803 ( 18) link_ALPHA1-3 : bond 0.00962 ( 7) link_ALPHA1-3 : angle 2.08669 ( 21) link_ALPHA1-6 : bond 0.00651 ( 6) link_ALPHA1-6 : angle 1.79590 ( 18) link_BETA1-4 : bond 0.00518 ( 65) link_BETA1-4 : angle 1.84806 ( 195) link_NAG-ASN : bond 0.00570 ( 46) link_NAG-ASN : angle 2.51028 ( 138) *********************** 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 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: E 104 MET cc_start: 0.9150 (tpp) cc_final: 0.8900 (tpp) REVERT: I 104 MET cc_start: 0.9262 (tmm) cc_final: 0.8665 (tmm) REVERT: K 70 MET cc_start: 0.7980 (mtm) cc_final: 0.7565 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1538 time to fit residues: 11.8765 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 135 optimal weight: 0.0870 chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.024206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.018650 restraints weight = 323022.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.019173 restraints weight = 196465.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.019524 restraints weight = 144916.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.019750 restraints weight = 120080.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.019894 restraints weight = 106647.279| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21367 Z= 0.113 Angle : 0.602 9.509 29301 Z= 0.282 Chirality : 0.044 0.269 3619 Planarity : 0.003 0.034 3492 Dihedral : 8.989 88.446 5328 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 aren not related in a simple way. whole: -0.23 (0.18), residues: 2415 helix: 1.43 (0.28), residues: 402 sheet: -0.45 (0.20), residues: 678 loop : -0.41 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 503 TYR 0.042 0.001 TYR L 51 PHE 0.010 0.001 PHE I 382 TRP 0.011 0.001 TRP J 631 HIS 0.005 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00240 (21198) covalent geometry : angle 0.56532 (28833) SS BOND : bond 0.00227 ( 39) SS BOND : angle 0.61860 ( 78) hydrogen bonds : bond 0.03532 ( 517) hydrogen bonds : angle 5.02613 ( 1416) link_ALPHA1-2 : bond 0.00350 ( 6) link_ALPHA1-2 : angle 1.96467 ( 18) link_ALPHA1-3 : bond 0.01151 ( 7) link_ALPHA1-3 : angle 1.75762 ( 21) link_ALPHA1-6 : bond 0.00861 ( 6) link_ALPHA1-6 : angle 1.38095 ( 18) link_BETA1-4 : bond 0.00476 ( 65) link_BETA1-4 : angle 1.65019 ( 195) link_NAG-ASN : bond 0.00314 ( 46) link_NAG-ASN : angle 2.20470 ( 138) *********************** 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 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8989 (pmm) cc_final: 0.8639 (pmm) REVERT: K 70 MET cc_start: 0.8017 (mtm) cc_final: 0.7573 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1459 time to fit residues: 11.5524 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.024125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.018588 restraints weight = 325576.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.019102 restraints weight = 199656.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.019437 restraints weight = 148555.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.019658 restraints weight = 123481.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.019802 restraints weight = 109965.613| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21367 Z= 0.146 Angle : 0.608 9.407 29301 Z= 0.286 Chirality : 0.044 0.270 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.732 89.605 5328 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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 aren not related in a simple way. whole: -0.24 (0.18), residues: 2415 helix: 1.55 (0.28), residues: 402 sheet: -0.57 (0.19), residues: 696 loop : -0.38 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 38 TYR 0.038 0.001 TYR L 51 PHE 0.012 0.001 PHE A 53 TRP 0.011 0.001 TRP B 614 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00315 (21198) covalent geometry : angle 0.56994 (28833) SS BOND : bond 0.00229 ( 39) SS BOND : angle 0.58527 ( 78) hydrogen bonds : bond 0.03551 ( 517) hydrogen bonds : angle 4.99661 ( 1416) link_ALPHA1-2 : bond 0.00471 ( 6) link_ALPHA1-2 : angle 2.00410 ( 18) link_ALPHA1-3 : bond 0.01090 ( 7) link_ALPHA1-3 : angle 1.83303 ( 21) link_ALPHA1-6 : bond 0.00770 ( 6) link_ALPHA1-6 : angle 1.36470 ( 18) link_BETA1-4 : bond 0.00478 ( 65) link_BETA1-4 : angle 1.69646 ( 195) link_NAG-ASN : bond 0.00372 ( 46) link_NAG-ASN : angle 2.25583 ( 138) *********************** 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 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8400 (tmm) cc_final: 0.8150 (tmm) REVERT: K 70 MET cc_start: 0.7929 (mtm) cc_final: 0.7536 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1312 time to fit residues: 10.5780 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 90 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.024246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.018729 restraints weight = 322174.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.019248 restraints weight = 196945.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.019595 restraints weight = 145619.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.019821 restraints weight = 120859.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.019964 restraints weight = 107302.270| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21367 Z= 0.119 Angle : 0.585 9.199 29301 Z= 0.275 Chirality : 0.043 0.273 3619 Planarity : 0.003 0.034 3492 Dihedral : 8.455 88.972 5328 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2415 helix: 1.93 (0.29), residues: 384 sheet: -0.58 (0.19), residues: 708 loop : -0.27 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 503 TYR 0.034 0.001 TYR L 51 PHE 0.009 0.001 PHE A 382 TRP 0.030 0.001 TRP E 112 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00257 (21198) covalent geometry : angle 0.54915 (28833) SS BOND : bond 0.00211 ( 39) SS BOND : angle 0.57131 ( 78) hydrogen bonds : bond 0.03387 ( 517) hydrogen bonds : angle 4.87090 ( 1416) link_ALPHA1-2 : bond 0.00393 ( 6) link_ALPHA1-2 : angle 1.94639 ( 18) link_ALPHA1-3 : bond 0.01094 ( 7) link_ALPHA1-3 : angle 1.73737 ( 21) link_ALPHA1-6 : bond 0.00803 ( 6) link_ALPHA1-6 : angle 1.28983 ( 18) link_BETA1-4 : bond 0.00470 ( 65) link_BETA1-4 : angle 1.62728 ( 195) link_NAG-ASN : bond 0.00309 ( 46) link_NAG-ASN : angle 2.15737 ( 138) *********************** 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 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8964 (pmm) cc_final: 0.8719 (pmm) REVERT: I 104 MET cc_start: 0.8942 (tmm) cc_final: 0.8625 (tmm) REVERT: K 70 MET cc_start: 0.7992 (mtm) cc_final: 0.7594 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1453 time to fit residues: 11.8631 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 0.6980 chunk 216 optimal weight: 20.0000 chunk 75 optimal weight: 0.0970 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 209 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.024351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.018836 restraints weight = 323330.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.019364 restraints weight = 196826.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.019716 restraints weight = 145244.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.019948 restraints weight = 120049.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.020099 restraints weight = 106283.760| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21367 Z= 0.100 Angle : 0.568 8.950 29301 Z= 0.267 Chirality : 0.043 0.277 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.082 87.558 5328 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 aren not related in a simple way. whole: -0.03 (0.18), residues: 2415 helix: 1.91 (0.29), residues: 387 sheet: -0.42 (0.19), residues: 717 loop : -0.29 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.031 0.001 TYR L 51 PHE 0.007 0.001 PHE A 382 TRP 0.019 0.001 TRP E 112 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00213 (21198) covalent geometry : angle 0.53325 (28833) SS BOND : bond 0.00199 ( 39) SS BOND : angle 0.53530 ( 78) hydrogen bonds : bond 0.03165 ( 517) hydrogen bonds : angle 4.73836 ( 1416) link_ALPHA1-2 : bond 0.00348 ( 6) link_ALPHA1-2 : angle 1.87511 ( 18) link_ALPHA1-3 : bond 0.01111 ( 7) link_ALPHA1-3 : angle 1.69744 ( 21) link_ALPHA1-6 : bond 0.00798 ( 6) link_ALPHA1-6 : angle 1.24907 ( 18) link_BETA1-4 : bond 0.00469 ( 65) link_BETA1-4 : angle 1.56720 ( 195) link_NAG-ASN : bond 0.00287 ( 46) link_NAG-ASN : angle 2.07099 ( 138) ********************** 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 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.8054 (mpp) cc_final: 0.7728 (ptp) REVERT: C 48 MET cc_start: 0.8946 (pmm) cc_final: 0.8728 (pmm) REVERT: I 104 MET cc_start: 0.8869 (tmm) cc_final: 0.8536 (tmm) REVERT: K 70 MET cc_start: 0.7978 (mtm) cc_final: 0.7590 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1411 time to fit residues: 11.6079 Evaluate side-chains 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 14 optimal weight: 0.0070 chunk 197 optimal weight: 9.9990 chunk 148 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 236 optimal weight: 40.0000 chunk 132 optimal weight: 0.0670 overall best weight: 1.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.024343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.018824 restraints weight = 322107.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.019351 restraints weight = 196191.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.019701 restraints weight = 144780.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.019929 restraints weight = 119883.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.020079 restraints weight = 106359.428| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21367 Z= 0.105 Angle : 0.561 8.914 29301 Z= 0.264 Chirality : 0.043 0.275 3619 Planarity : 0.003 0.032 3492 Dihedral : 7.925 89.082 5328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 aren not related in a simple way. whole: 0.04 (0.18), residues: 2415 helix: 1.95 (0.29), residues: 387 sheet: -0.37 (0.19), residues: 732 loop : -0.24 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.030 0.001 TYR L 51 PHE 0.008 0.001 PHE I 382 TRP 0.023 0.001 TRP E 112 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00226 (21198) covalent geometry : angle 0.52579 (28833) SS BOND : bond 0.00198 ( 39) SS BOND : angle 0.52053 ( 78) hydrogen bonds : bond 0.03121 ( 517) hydrogen bonds : angle 4.68999 ( 1416) link_ALPHA1-2 : bond 0.00369 ( 6) link_ALPHA1-2 : angle 1.89036 ( 18) link_ALPHA1-3 : bond 0.01056 ( 7) link_ALPHA1-3 : angle 1.68072 ( 21) link_ALPHA1-6 : bond 0.00770 ( 6) link_ALPHA1-6 : angle 1.24380 ( 18) link_BETA1-4 : bond 0.00470 ( 65) link_BETA1-4 : angle 1.56952 ( 195) link_NAG-ASN : bond 0.00291 ( 46) link_NAG-ASN : angle 2.07082 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.35 seconds wall clock time: 47 minutes 26.93 seconds (2846.93 seconds total)