Starting phenix.real_space_refine on Thu Mar 5 22:38:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ozc_20224/03_2026/6ozc_20224.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 150 5.16 5 C 16083 2.51 5 N 4164 2.21 5 O 5424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25821 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "F" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "R" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "P" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" 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: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" 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: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "f" 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: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "h" 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: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" 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: "o" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "r" 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: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "G" 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.73, per 1000 atoms: 0.22 Number of scatterers: 25821 At special positions: 0 Unit cell: (188.64, 197.81, 137.55, 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 150 16.00 O 5424 8.00 N 4164 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " 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=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.07 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.12 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN W 5 " - " MAN W 6 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN c 4 " - " MAN c 5 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN g 5 " - " MAN g 6 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN m 4 " - " MAN m 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN q 5 " - " MAN q 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 5 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 7 " - " MAN e 8 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 8 " " MAN i 4 " - " MAN i 5 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 8 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 7 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 7 " " MAN e 7 " - " MAN e 9 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 7 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 7 " " BMA m 3 " - " MAN m 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 7 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG 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 s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 626 " - " ASN A 133 " " NAG A 653 " - " ASN A 234 " " NAG A 656 " - " ASN A 160 " " NAG A 659 " - " ASN A 197 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 626 " - " ASN E 133 " " NAG E 653 " - " ASN E 234 " " NAG E 656 " - " ASN E 160 " " NAG E 659 " - " ASN E 197 " " NAG F 626 " - " ASN F 133 " " NAG F 653 " - " ASN F 234 " " NAG F 656 " - " ASN F 160 " " NAG F 659 " - " ASN F 197 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 339 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 392 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 339 " " NAG j 1 " - " ASN E 448 " " NAG k 1 " - " ASN E 301 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN F 262 " " NAG n 1 " - " ASN F 363 " " NAG o 1 " - " ASN F 392 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 332 " " NAG r 1 " - " ASN F 295 " " NAG s 1 " - " ASN F 339 " " NAG t 1 " - " ASN F 448 " " NAG u 1 " - " ASN F 301 " " NAG v 1 " - " ASN F 156 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 905.1 milliseconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 66 sheets defined 18.1% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 4.063A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 661 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 52A through 55 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 52A through 55 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU I 592 " --> pdb=" O ARG I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 661 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 55 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 52A through 55 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A 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 removed outlier: 6.535A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 495 through 498 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.636A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.536A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 495 through 498 Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AF2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF3, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AF4, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AF5, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 358 through 361 Processing sheet with id=AF7, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 416 Processing sheet with id=AF8, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AG1, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.663A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2421 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5455 1.32 - 1.45: 8504 1.45 - 1.59: 12135 1.59 - 1.72: 21 1.72 - 1.86: 198 Bond restraints: 26313 Sorted by residual: bond pdb=" C1 NAG F 659 " pdb=" O5 NAG F 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C1 NAG A 659 " pdb=" O5 NAG A 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C1 NAG E 659 " pdb=" O5 NAG E 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C THR B 627 " pdb=" N TRP B 628 " ideal model delta sigma weight residual 1.335 1.247 0.087 1.25e-02 6.40e+03 4.90e+01 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.89e+01 ... (remaining 26308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 30330 2.50 - 5.00: 4658 5.00 - 7.50: 658 7.50 - 10.00: 57 10.00 - 12.51: 9 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N ARG J 66 " pdb=" CA ARG J 66 " pdb=" C ARG J 66 " ideal model delta sigma weight residual 113.88 101.37 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG C 66 " pdb=" CA ARG C 66 " pdb=" C ARG C 66 " ideal model delta sigma weight residual 113.88 101.38 12.50 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG K 66 " pdb=" CA ARG K 66 " pdb=" C ARG K 66 " ideal model delta sigma weight residual 113.88 101.40 12.48 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N HIS E 72 " pdb=" CA HIS E 72 " pdb=" C HIS E 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 angle pdb=" N HIS F 72 " pdb=" CA HIS F 72 " pdb=" C HIS F 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 17157 21.93 - 43.86: 489 43.86 - 65.79: 150 65.79 - 87.73: 135 87.73 - 109.66: 87 Dihedral angle restraints: 18018 sinusoidal: 9357 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.36 -40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.35 -40.35 1 1.00e+01 1.00e-02 2.28e+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 93.00 133.34 -40.34 1 1.00e+01 1.00e-02 2.28e+01 ... (remaining 18015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3436 0.115 - 0.229: 1000 0.229 - 0.344: 127 0.344 - 0.459: 18 0.459 - 0.573: 21 Chirality restraints: 4602 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 4599 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.42e+01 pdb=" C7 NAG Z 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.41e+01 pdb=" C7 NAG t 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG t 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG t 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG t 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.063 2.00e-02 2.50e+03 5.21e-02 3.40e+01 pdb=" C7 NAG j 1 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8160 2.82 - 3.34: 23259 3.34 - 3.86: 43967 3.86 - 4.38: 51813 4.38 - 4.90: 83268 Nonbonded interactions: 210467 Sorted by model distance: nonbonded pdb=" O4 NAG A 659 " pdb=" O6 NAG A 659 " model vdw 2.303 3.040 nonbonded pdb=" O4 NAG E 659 " pdb=" O6 NAG E 659 " model vdw 2.304 3.040 nonbonded pdb=" O4 NAG F 659 " pdb=" O6 NAG F 659 " model vdw 2.304 3.040 nonbonded pdb=" O LEU G 568 " pdb=" OG1 THR G 569 " model vdw 2.340 3.040 nonbonded pdb=" O LEU I 568 " pdb=" OG1 THR I 569 " model vdw 2.341 3.040 ... (remaining 210462 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'd' selection = chain 'f' selection = chain 'n' selection = chain 'p' } ncs_group { reference = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'W' and (resid 1 or resid 4 through 8)) selection = (chain 'Y' and (resid 2 or resid 5 through 9)) selection = (chain 'e' and (resid 2 or resid 5 through 9)) selection = (chain 'g' and (resid 1 or resid 4 through 8)) selection = (chain 'i' and (resid 2 or resid 5 through 9)) selection = (chain 'o' and (resid 2 or resid 5 through 9)) selection = (chain 'q' and (resid 1 or resid 4 through 8)) selection = (chain 's' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 't' selection = chain 'u' 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.780 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.212 26541 Z= 1.203 Angle : 1.869 12.505 36354 Z= 1.152 Chirality : 0.110 0.573 4602 Planarity : 0.009 0.052 4233 Dihedral : 15.750 109.656 12330 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.13 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2967 helix: -1.25 (0.22), residues: 393 sheet: 0.81 (0.14), residues: 1107 loop : 0.41 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 38 TYR 0.077 0.010 TYR K 91 PHE 0.047 0.007 PHE D 71 TRP 0.061 0.009 TRP D 35 HIS 0.011 0.003 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.02283 (26313) covalent geometry : angle 1.84033 (35712) SS BOND : bond 0.02554 ( 42) SS BOND : angle 3.00778 ( 84) hydrogen bonds : bond 0.16104 ( 909) hydrogen bonds : angle 7.86563 ( 2421) link_ALPHA1-2 : bond 0.03788 ( 24) link_ALPHA1-2 : angle 2.38211 ( 72) link_ALPHA1-3 : bond 0.03730 ( 30) link_ALPHA1-3 : angle 3.60087 ( 90) link_ALPHA1-6 : bond 0.03088 ( 30) link_ALPHA1-6 : angle 2.89907 ( 90) link_BETA1-4 : bond 0.03015 ( 51) link_BETA1-4 : angle 3.11162 ( 153) link_NAG-ASN : bond 0.03377 ( 51) link_NAG-ASN : angle 3.13175 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9309 (tpp) cc_final: 0.8883 (tpt) REVERT: A 377 ASN cc_start: 0.8428 (t0) cc_final: 0.7977 (p0) REVERT: A 491 ILE cc_start: 0.8624 (mp) cc_final: 0.8389 (tp) REVERT: B 535 MET cc_start: 0.8445 (mtt) cc_final: 0.7983 (tpt) REVERT: L 42 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8187 (pttt) REVERT: L 55 LYS cc_start: 0.8089 (tttm) cc_final: 0.7764 (tttt) REVERT: L 79 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7235 (tm-30) REVERT: H 2 VAL cc_start: 0.7847 (t) cc_final: 0.7575 (p) REVERT: H 26 ASN cc_start: 0.8214 (m-40) cc_final: 0.7699 (m-40) REVERT: D 33 LEU cc_start: 0.6981 (tt) cc_final: 0.6481 (tt) REVERT: D 61 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8123 (mtm-85) REVERT: D 82 ASP cc_start: 0.8349 (m-30) cc_final: 0.7226 (m-30) REVERT: C 26 ASN cc_start: 0.8534 (m-40) cc_final: 0.8050 (m-40) REVERT: C 29 ILE cc_start: 0.8544 (pt) cc_final: 0.7914 (mm) REVERT: C 34 MET cc_start: 0.8751 (mmm) cc_final: 0.8321 (mmm) REVERT: C 76 ASP cc_start: 0.8127 (m-30) cc_final: 0.7670 (m-30) REVERT: E 377 ASN cc_start: 0.8469 (t0) cc_final: 0.8086 (p0) REVERT: G 601 LYS cc_start: 0.8702 (pttm) cc_final: 0.8297 (pttm) REVERT: Q 42 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8370 (pttt) REVERT: Q 79 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7033 (tm-30) REVERT: O 26 ASN cc_start: 0.8248 (m-40) cc_final: 0.8004 (m-40) REVERT: M 33 LEU cc_start: 0.7093 (tt) cc_final: 0.6674 (tt) REVERT: M 61 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: M 82 ASP cc_start: 0.8624 (m-30) cc_final: 0.7530 (m-30) REVERT: J 26 ASN cc_start: 0.7912 (m-40) cc_final: 0.7528 (m-40) REVERT: J 34 MET cc_start: 0.8666 (mmm) cc_final: 0.8356 (mmm) REVERT: J 72 ASP cc_start: 0.6786 (t0) cc_final: 0.5420 (t70) REVERT: F 122 LEU cc_start: 0.9254 (mt) cc_final: 0.9041 (mm) REVERT: F 125 LEU cc_start: 0.9153 (mp) cc_final: 0.8940 (tp) REVERT: F 161 MET cc_start: 0.9213 (tpp) cc_final: 0.8485 (tpt) REVERT: R 42 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7978 (pttt) REVERT: R 78 LEU cc_start: 0.8553 (tp) cc_final: 0.8332 (tp) REVERT: R 79 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6917 (tm-30) REVERT: P 26 ASN cc_start: 0.8142 (m-40) cc_final: 0.7795 (m-40) REVERT: N 61 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7779 (mtm-85) REVERT: N 80 PHE cc_start: 0.8796 (m-80) cc_final: 0.8580 (m-80) REVERT: N 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.7432 (m-30) REVERT: N 91 TYR cc_start: 0.4513 (p90) cc_final: 0.4099 (p90) REVERT: N 100 GLN cc_start: 0.9065 (pm20) cc_final: 0.8770 (pm20) REVERT: K 26 ASN cc_start: 0.7822 (m-40) cc_final: 0.7455 (m-40) REVERT: K 29 ILE cc_start: 0.8614 (pt) cc_final: 0.8133 (mm) REVERT: K 34 MET cc_start: 0.8601 (mmm) cc_final: 0.8142 (mmm) REVERT: K 72 ASP cc_start: 0.7018 (t0) cc_final: 0.4943 (t0) REVERT: K 76 ASP cc_start: 0.8219 (m-30) cc_final: 0.7714 (m-30) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.1887 time to fit residues: 204.6075 Evaluate side-chains 336 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 590 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 656 ASN ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 195 ASN F 328 GLN I 575 GLN I 616 ASN ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063111 restraints weight = 89789.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065626 restraints weight = 43556.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067301 restraints weight = 28742.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068345 restraints weight = 22345.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068960 restraints weight = 19212.394| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26541 Z= 0.199 Angle : 0.857 8.580 36354 Z= 0.431 Chirality : 0.050 0.244 4602 Planarity : 0.005 0.092 4233 Dihedral : 13.040 85.377 6939 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.72 % Favored : 94.91 % Rotamer: Outliers : 2.65 % Allowed : 9.02 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2967 helix: 0.10 (0.27), residues: 372 sheet: 0.63 (0.14), residues: 1077 loop : -0.05 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 24 TYR 0.026 0.002 TYR Q 49 PHE 0.023 0.003 PHE D 71 TRP 0.025 0.002 TRP M 35 HIS 0.008 0.001 HIS Q 90 Details of bonding type rmsd covalent geometry : bond 0.00430 (26313) covalent geometry : angle 0.82020 (35712) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.25085 ( 84) hydrogen bonds : bond 0.05731 ( 909) hydrogen bonds : angle 6.62686 ( 2421) link_ALPHA1-2 : bond 0.00420 ( 24) link_ALPHA1-2 : angle 1.70750 ( 72) link_ALPHA1-3 : bond 0.00835 ( 30) link_ALPHA1-3 : angle 2.44944 ( 90) link_ALPHA1-6 : bond 0.00877 ( 30) link_ALPHA1-6 : angle 2.16212 ( 90) link_BETA1-4 : bond 0.00467 ( 51) link_BETA1-4 : angle 2.19481 ( 153) link_NAG-ASN : bond 0.00402 ( 51) link_NAG-ASN : angle 2.04933 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 423 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7956 (mtm) cc_final: 0.7753 (mtm) REVERT: A 271 MET cc_start: 0.7894 (mmm) cc_final: 0.7542 (mmm) REVERT: B 535 MET cc_start: 0.8449 (mtt) cc_final: 0.8235 (tpt) REVERT: B 543 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7306 (t0) REVERT: B 584 GLU cc_start: 0.8657 (tt0) cc_final: 0.8170 (tm-30) REVERT: B 625 ASN cc_start: 0.8775 (m110) cc_final: 0.8324 (m-40) REVERT: B 641 ILE cc_start: 0.8978 (mp) cc_final: 0.8761 (pt) REVERT: B 651 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7828 (p0) REVERT: B 659 ASP cc_start: 0.8064 (m-30) cc_final: 0.7737 (t70) REVERT: L 4 MET cc_start: 0.7083 (ttp) cc_final: 0.6825 (ttp) REVERT: L 42 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8400 (mmmt) REVERT: L 75 ILE cc_start: 0.7188 (mt) cc_final: 0.6901 (mm) REVERT: L 79 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7518 (tm-30) REVERT: H 79 TYR cc_start: 0.7864 (m-80) cc_final: 0.7261 (m-10) REVERT: D 33 LEU cc_start: 0.6145 (tt) cc_final: 0.5721 (tt) REVERT: C 34 MET cc_start: 0.8607 (mmm) cc_final: 0.8182 (mmm) REVERT: C 75 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7341 (mm-30) REVERT: C 76 ASP cc_start: 0.8087 (m-30) cc_final: 0.7883 (m-30) REVERT: E 434 MET cc_start: 0.8535 (ttp) cc_final: 0.8037 (ttp) REVERT: G 535 MET cc_start: 0.7628 (tpt) cc_final: 0.6937 (tpp) REVERT: G 542 ARG cc_start: 0.7663 (ttt-90) cc_final: 0.7125 (mtt-85) REVERT: G 625 ASN cc_start: 0.9082 (m-40) cc_final: 0.8639 (m-40) REVERT: G 651 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7543 (p0) REVERT: O 26 ASN cc_start: 0.7903 (m-40) cc_final: 0.7577 (m110) REVERT: O 72 ASP cc_start: 0.7855 (t0) cc_final: 0.7517 (m-30) REVERT: O 79 TYR cc_start: 0.7855 (m-80) cc_final: 0.7566 (m-10) REVERT: O 82 MET cc_start: 0.7541 (mtp) cc_final: 0.6882 (ttm) REVERT: J 82 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9149 (mtmm) REVERT: J 100 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6465 (m-30) REVERT: F 104 MET cc_start: 0.8544 (tpp) cc_final: 0.8007 (tpp) REVERT: F 161 MET cc_start: 0.8844 (tpp) cc_final: 0.8502 (tpt) REVERT: I 535 MET cc_start: 0.8196 (tpt) cc_final: 0.7814 (mmm) REVERT: I 584 GLU cc_start: 0.8430 (tt0) cc_final: 0.8110 (tm-30) REVERT: I 649 SER cc_start: 0.8959 (m) cc_final: 0.8482 (p) REVERT: R 78 LEU cc_start: 0.8801 (tp) cc_final: 0.8314 (pp) REVERT: R 79 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7139 (tm-30) REVERT: P 26 ASN cc_start: 0.7806 (m-40) cc_final: 0.7595 (m-40) REVERT: P 72 ASP cc_start: 0.7743 (t0) cc_final: 0.7468 (m-30) REVERT: P 79 TYR cc_start: 0.7647 (m-80) cc_final: 0.7335 (m-10) REVERT: P 99 ARG cc_start: 0.8176 (tpm170) cc_final: 0.7934 (tpm170) REVERT: N 91 TYR cc_start: 0.4865 (p90) cc_final: 0.4374 (p90) REVERT: K 34 MET cc_start: 0.8503 (mmm) cc_final: 0.7739 (mmm) REVERT: K 72 ASP cc_start: 0.6594 (t0) cc_final: 0.6355 (t0) REVERT: K 82 LYS cc_start: 0.9397 (mmmt) cc_final: 0.9185 (mtmm) outliers start: 69 outliers final: 33 residues processed: 464 average time/residue: 0.1675 time to fit residues: 119.9605 Evaluate side-chains 336 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 127 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 209 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 195 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN Q 79 GLN O 81 GLN M 79 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN F 377 ASN I 653 GLN P 81 GLN N 79 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059890 restraints weight = 90518.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062325 restraints weight = 44495.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063909 restraints weight = 29717.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064935 restraints weight = 23450.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065551 restraints weight = 20287.884| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26541 Z= 0.225 Angle : 0.796 8.684 36354 Z= 0.392 Chirality : 0.048 0.266 4602 Planarity : 0.005 0.069 4233 Dihedral : 11.133 78.787 6939 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.12 % Favored : 94.78 % Rotamer: Outliers : 2.65 % Allowed : 11.64 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2967 helix: 0.68 (0.29), residues: 339 sheet: 0.44 (0.15), residues: 1014 loop : -0.29 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 39 TYR 0.024 0.002 TYR R 91 PHE 0.025 0.003 PHE M 98 TRP 0.022 0.002 TRP F 112 HIS 0.020 0.002 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00512 (26313) covalent geometry : angle 0.76139 (35712) SS BOND : bond 0.00536 ( 42) SS BOND : angle 1.05292 ( 84) hydrogen bonds : bond 0.04708 ( 909) hydrogen bonds : angle 6.28521 ( 2421) link_ALPHA1-2 : bond 0.00230 ( 24) link_ALPHA1-2 : angle 2.04420 ( 72) link_ALPHA1-3 : bond 0.00780 ( 30) link_ALPHA1-3 : angle 2.17597 ( 90) link_ALPHA1-6 : bond 0.00894 ( 30) link_ALPHA1-6 : angle 2.16162 ( 90) link_BETA1-4 : bond 0.00526 ( 51) link_BETA1-4 : angle 1.83080 ( 153) link_NAG-ASN : bond 0.00414 ( 51) link_NAG-ASN : angle 1.90197 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 318 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8997 (tpp) cc_final: 0.8433 (tpp) REVERT: A 217 TYR cc_start: 0.8578 (m-80) cc_final: 0.8091 (m-80) REVERT: B 584 GLU cc_start: 0.8697 (tt0) cc_final: 0.8225 (tm-30) REVERT: B 651 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7893 (p0) REVERT: B 659 ASP cc_start: 0.7858 (m-30) cc_final: 0.7399 (t0) REVERT: L 4 MET cc_start: 0.7341 (ttp) cc_final: 0.7086 (ttp) REVERT: L 79 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7381 (tm-30) REVERT: H 68 THR cc_start: 0.8946 (m) cc_final: 0.8561 (t) REVERT: H 72 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: H 79 TYR cc_start: 0.7850 (m-80) cc_final: 0.7370 (m-10) REVERT: H 100 ASN cc_start: 0.7726 (m-40) cc_final: 0.7456 (t0) REVERT: D 54 LEU cc_start: 0.8704 (pp) cc_final: 0.8422 (tt) REVERT: C 26 ASN cc_start: 0.8163 (m110) cc_final: 0.7893 (m110) REVERT: C 34 MET cc_start: 0.8610 (mmm) cc_final: 0.8102 (mmm) REVERT: C 100 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7241 (t0) REVERT: E 137 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7310 (p0) REVERT: E 434 MET cc_start: 0.8550 (ttp) cc_final: 0.8125 (ttp) REVERT: G 535 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7635 (mmt) REVERT: G 542 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7152 (mtt-85) REVERT: G 601 LYS cc_start: 0.9150 (pttm) cc_final: 0.8906 (pttt) REVERT: G 625 ASN cc_start: 0.9008 (m-40) cc_final: 0.8619 (m-40) REVERT: Q 48 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7636 (mm) REVERT: O 26 ASN cc_start: 0.8113 (m-40) cc_final: 0.7852 (m110) REVERT: O 72 ASP cc_start: 0.7913 (t0) cc_final: 0.7603 (m-30) REVERT: O 79 TYR cc_start: 0.8181 (m-80) cc_final: 0.7584 (m-10) REVERT: O 82 MET cc_start: 0.7541 (mtp) cc_final: 0.7314 (ttm) REVERT: M 33 LEU cc_start: 0.6095 (tt) cc_final: 0.5805 (tt) REVERT: M 103 ARG cc_start: 0.8327 (mpp-170) cc_final: 0.7595 (tpp80) REVERT: J 82 MET cc_start: 0.6500 (mtm) cc_final: 0.5890 (mtp) REVERT: J 100 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: F 104 MET cc_start: 0.8767 (tpp) cc_final: 0.8052 (tpp) REVERT: I 535 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7550 (mmm) REVERT: I 648 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8523 (pp20) REVERT: I 649 SER cc_start: 0.9027 (m) cc_final: 0.8756 (p) REVERT: R 42 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8557 (mmtp) REVERT: R 78 LEU cc_start: 0.8808 (tp) cc_final: 0.8370 (pp) REVERT: R 79 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6905 (tm-30) REVERT: P 26 ASN cc_start: 0.7555 (m-40) cc_final: 0.7286 (m-40) REVERT: P 36 TRP cc_start: 0.7856 (m100) cc_final: 0.7599 (m100) REVERT: P 79 TYR cc_start: 0.8098 (m-80) cc_final: 0.7803 (m-10) REVERT: N 54 LEU cc_start: 0.8685 (pp) cc_final: 0.8426 (tt) REVERT: K 34 MET cc_start: 0.8587 (mmm) cc_final: 0.8242 (mmm) REVERT: K 85 GLU cc_start: 0.8357 (mp0) cc_final: 0.8100 (tp30) outliers start: 69 outliers final: 33 residues processed: 366 average time/residue: 0.1620 time to fit residues: 93.8901 Evaluate side-chains 308 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain N residue 87 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 241 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN L 100 GLN D 37 GLN D 89 GLN D 90 HIS E 195 ASN E 328 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 130 GLN F 195 ASN F 328 GLN I 575 GLN I 590 GLN I 652 GLN R 89 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.057248 restraints weight = 91072.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059565 restraints weight = 45767.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061077 restraints weight = 30962.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062006 restraints weight = 24598.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062609 restraints weight = 21466.576| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 26541 Z= 0.288 Angle : 0.853 10.163 36354 Z= 0.413 Chirality : 0.051 0.290 4602 Planarity : 0.005 0.068 4233 Dihedral : 10.166 70.259 6939 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 4.26 % Allowed : 10.79 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2967 helix: 0.19 (0.28), residues: 351 sheet: 0.36 (0.16), residues: 942 loop : -0.42 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 57 TYR 0.021 0.002 TYR R 49 PHE 0.028 0.003 PHE D 71 TRP 0.023 0.002 TRP A 112 HIS 0.025 0.002 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00657 (26313) covalent geometry : angle 0.81687 (35712) SS BOND : bond 0.00581 ( 42) SS BOND : angle 1.20137 ( 84) hydrogen bonds : bond 0.04703 ( 909) hydrogen bonds : angle 6.31004 ( 2421) link_ALPHA1-2 : bond 0.00294 ( 24) link_ALPHA1-2 : angle 2.43785 ( 72) link_ALPHA1-3 : bond 0.00765 ( 30) link_ALPHA1-3 : angle 2.37410 ( 90) link_ALPHA1-6 : bond 0.00809 ( 30) link_ALPHA1-6 : angle 2.16155 ( 90) link_BETA1-4 : bond 0.00482 ( 51) link_BETA1-4 : angle 1.74660 ( 153) link_NAG-ASN : bond 0.00604 ( 51) link_NAG-ASN : angle 2.07618 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 290 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8959 (tpp) cc_final: 0.8245 (tpp) REVERT: B 535 MET cc_start: 0.7883 (tpt) cc_final: 0.7316 (mmt) REVERT: B 659 ASP cc_start: 0.7718 (m-30) cc_final: 0.7297 (t0) REVERT: L 4 MET cc_start: 0.8025 (ttp) cc_final: 0.7751 (ttp) REVERT: L 79 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7394 (tm-30) REVERT: H 72 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: H 99 ARG cc_start: 0.8082 (tpm170) cc_final: 0.7865 (tpp-160) REVERT: D 39 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7245 (mmtm) REVERT: D 54 LEU cc_start: 0.8756 (pp) cc_final: 0.8474 (tt) REVERT: D 103 ARG cc_start: 0.8660 (ptp90) cc_final: 0.8186 (mpp-170) REVERT: C 19 ILE cc_start: 0.8543 (mm) cc_final: 0.8326 (mm) REVERT: C 34 MET cc_start: 0.8674 (mmm) cc_final: 0.8019 (mmm) REVERT: C 72 ASP cc_start: 0.8178 (m-30) cc_final: 0.7616 (m-30) REVERT: C 100 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.5911 (t0) REVERT: C 100 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8050 (t0) REVERT: E 137 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8187 (p0) REVERT: E 434 MET cc_start: 0.8695 (ttp) cc_final: 0.8160 (ttp) REVERT: G 535 MET cc_start: 0.7864 (tpt) cc_final: 0.7601 (mmm) REVERT: G 542 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.7181 (mtt-85) REVERT: G 601 LYS cc_start: 0.9107 (pttm) cc_final: 0.8575 (pttm) REVERT: G 625 ASN cc_start: 0.8954 (m-40) cc_final: 0.8633 (m-40) REVERT: G 626 MET cc_start: 0.7749 (tmm) cc_final: 0.7382 (tmm) REVERT: G 651 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7907 (p0) REVERT: Q 4 MET cc_start: 0.7988 (ttp) cc_final: 0.7662 (tmm) REVERT: Q 48 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7779 (mm) REVERT: Q 58 VAL cc_start: 0.7529 (t) cc_final: 0.7032 (t) REVERT: O 26 ASN cc_start: 0.7836 (m-40) cc_final: 0.7510 (m110) REVERT: O 79 TYR cc_start: 0.8334 (m-80) cc_final: 0.8059 (m-10) REVERT: O 82 MET cc_start: 0.7651 (mtp) cc_final: 0.7277 (ttm) REVERT: M 103 ARG cc_start: 0.8616 (mpp-170) cc_final: 0.7813 (tpp80) REVERT: J 19 ILE cc_start: 0.8429 (mm) cc_final: 0.8213 (mm) REVERT: J 38 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6875 (ttm-80) REVERT: J 100 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7894 (t0) REVERT: F 195 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7564 (t0) REVERT: I 535 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: I 584 GLU cc_start: 0.8438 (tt0) cc_final: 0.8112 (tm-30) REVERT: I 601 LYS cc_start: 0.9219 (pttm) cc_final: 0.8631 (pttm) REVERT: I 648 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8603 (pp20) REVERT: R 42 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8594 (mmtp) REVERT: R 78 LEU cc_start: 0.8820 (tp) cc_final: 0.8552 (tp) REVERT: P 26 ASN cc_start: 0.7574 (m-40) cc_final: 0.7232 (m110) REVERT: P 82 MET cc_start: 0.7595 (mmp) cc_final: 0.7334 (mmp) REVERT: N 54 LEU cc_start: 0.8860 (pp) cc_final: 0.8642 (tt) REVERT: N 88 CYS cc_start: 0.2377 (t) cc_final: 0.1957 (t) REVERT: K 19 ILE cc_start: 0.8623 (mm) cc_final: 0.8409 (mm) REVERT: K 34 MET cc_start: 0.8620 (mmm) cc_final: 0.8150 (mmm) REVERT: K 100 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7997 (t0) REVERT: K 110 THR cc_start: 0.8432 (m) cc_final: 0.7964 (p) outliers start: 111 outliers final: 68 residues processed: 370 average time/residue: 0.1557 time to fit residues: 90.5383 Evaluate side-chains 337 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 257 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 287 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 590 GLN E 130 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN F 195 ASN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN P 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058878 restraints weight = 90065.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.061288 restraints weight = 44459.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062861 restraints weight = 29752.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063839 restraints weight = 23464.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064406 restraints weight = 20374.649| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26541 Z= 0.160 Angle : 0.730 9.433 36354 Z= 0.352 Chirality : 0.047 0.301 4602 Planarity : 0.004 0.088 4233 Dihedral : 9.398 66.538 6939 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 3.23 % Allowed : 12.29 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2967 helix: 0.43 (0.28), residues: 366 sheet: 0.34 (0.16), residues: 966 loop : -0.49 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 83 TYR 0.020 0.001 TYR R 49 PHE 0.016 0.002 PHE D 71 TRP 0.018 0.001 TRP A 112 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00357 (26313) covalent geometry : angle 0.69793 (35712) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.08886 ( 84) hydrogen bonds : bond 0.04128 ( 909) hydrogen bonds : angle 6.01768 ( 2421) link_ALPHA1-2 : bond 0.00308 ( 24) link_ALPHA1-2 : angle 1.97469 ( 72) link_ALPHA1-3 : bond 0.00848 ( 30) link_ALPHA1-3 : angle 2.15633 ( 90) link_ALPHA1-6 : bond 0.00957 ( 30) link_ALPHA1-6 : angle 2.01424 ( 90) link_BETA1-4 : bond 0.00347 ( 51) link_BETA1-4 : angle 1.51983 ( 153) link_NAG-ASN : bond 0.00304 ( 51) link_NAG-ASN : angle 1.71997 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8901 (tpp) cc_final: 0.8209 (tpp) REVERT: B 535 MET cc_start: 0.7818 (tpt) cc_final: 0.7214 (mmt) REVERT: B 651 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7951 (p0) REVERT: L 4 MET cc_start: 0.8013 (ttp) cc_final: 0.7709 (ttp) REVERT: L 79 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7429 (tm-30) REVERT: H 68 THR cc_start: 0.9070 (m) cc_final: 0.8726 (p) REVERT: H 72 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: H 82 MET cc_start: 0.7810 (mtp) cc_final: 0.7588 (ttm) REVERT: H 99 ARG cc_start: 0.8056 (tpm170) cc_final: 0.7795 (mmm160) REVERT: D 103 ARG cc_start: 0.8627 (ptp90) cc_final: 0.8140 (mpp-170) REVERT: C 34 MET cc_start: 0.8673 (mmm) cc_final: 0.8159 (mmm) REVERT: C 72 ASP cc_start: 0.8015 (m-30) cc_final: 0.7609 (m-30) REVERT: C 100 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7818 (t0) REVERT: E 137 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8071 (p0) REVERT: E 434 MET cc_start: 0.8581 (ttp) cc_final: 0.8075 (ttp) REVERT: G 535 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7353 (mmt) REVERT: G 542 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7186 (mtt-85) REVERT: G 601 LYS cc_start: 0.9074 (pttm) cc_final: 0.8577 (pttm) REVERT: G 625 ASN cc_start: 0.8961 (m-40) cc_final: 0.8607 (m-40) REVERT: G 626 MET cc_start: 0.7343 (tmm) cc_final: 0.7029 (tmm) REVERT: Q 58 VAL cc_start: 0.7591 (t) cc_final: 0.7128 (t) REVERT: O 26 ASN cc_start: 0.7961 (m-40) cc_final: 0.7637 (m110) REVERT: O 68 THR cc_start: 0.9047 (m) cc_final: 0.8650 (p) REVERT: O 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7500 (m-30) REVERT: M 39 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6777 (mmtm) REVERT: M 103 ARG cc_start: 0.8681 (mpp-170) cc_final: 0.7877 (tpp80) REVERT: J 79 TYR cc_start: 0.8581 (m-80) cc_final: 0.8353 (m-80) REVERT: J 83 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.6879 (ttp-110) REVERT: J 100 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6099 (t0) REVERT: I 535 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7382 (mmm) REVERT: I 601 LYS cc_start: 0.9221 (pttm) cc_final: 0.8554 (ptpp) REVERT: I 647 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6740 (mt-10) REVERT: I 652 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8466 (pp30) REVERT: R 24 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7465 (tpt90) REVERT: P 26 ASN cc_start: 0.7790 (m-40) cc_final: 0.7563 (m110) REVERT: P 68 THR cc_start: 0.9021 (m) cc_final: 0.8569 (p) REVERT: P 82 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8538 (mtmm) REVERT: K 34 MET cc_start: 0.8633 (mmm) cc_final: 0.8122 (mmm) REVERT: K 100 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7766 (t0) REVERT: K 110 THR cc_start: 0.8400 (m) cc_final: 0.7919 (p) outliers start: 84 outliers final: 56 residues processed: 351 average time/residue: 0.1753 time to fit residues: 97.0518 Evaluate side-chains 324 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 258 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 HIS O 81 GLN M 37 GLN J 82AHIS F 195 ASN F 328 GLN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN N 90 HIS ** K 100CASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.057229 restraints weight = 91738.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059555 restraints weight = 45629.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061080 restraints weight = 30743.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062023 restraints weight = 24391.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062583 restraints weight = 21249.459| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26541 Z= 0.239 Angle : 0.783 8.255 36354 Z= 0.377 Chirality : 0.049 0.316 4602 Planarity : 0.005 0.080 4233 Dihedral : 9.110 60.246 6939 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 4.07 % Allowed : 12.79 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2967 helix: 0.33 (0.28), residues: 363 sheet: 0.20 (0.17), residues: 936 loop : -0.55 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 360 TYR 0.020 0.002 TYR R 49 PHE 0.018 0.002 PHE E 376 TRP 0.019 0.002 TRP A 112 HIS 0.007 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00545 (26313) covalent geometry : angle 0.74810 (35712) SS BOND : bond 0.00550 ( 42) SS BOND : angle 1.31468 ( 84) hydrogen bonds : bond 0.04345 ( 909) hydrogen bonds : angle 6.06232 ( 2421) link_ALPHA1-2 : bond 0.00260 ( 24) link_ALPHA1-2 : angle 2.29352 ( 72) link_ALPHA1-3 : bond 0.00775 ( 30) link_ALPHA1-3 : angle 2.19303 ( 90) link_ALPHA1-6 : bond 0.00888 ( 30) link_ALPHA1-6 : angle 2.02074 ( 90) link_BETA1-4 : bond 0.00408 ( 51) link_BETA1-4 : angle 1.64830 ( 153) link_NAG-ASN : bond 0.00507 ( 51) link_NAG-ASN : angle 1.92127 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 280 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8930 (tpp) cc_final: 0.8253 (tpp) REVERT: B 535 MET cc_start: 0.7647 (tpt) cc_final: 0.7239 (mmt) REVERT: B 584 GLU cc_start: 0.8675 (tt0) cc_final: 0.8350 (tm-30) REVERT: B 651 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7861 (p0) REVERT: L 78 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7053 (pp) REVERT: L 79 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7376 (tm-30) REVERT: H 68 THR cc_start: 0.9099 (m) cc_final: 0.8725 (p) REVERT: H 72 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: H 79 TYR cc_start: 0.7928 (m-80) cc_final: 0.7438 (m-10) REVERT: D 39 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7317 (mmtm) REVERT: D 42 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8344 (mmmm) REVERT: D 103 ARG cc_start: 0.8675 (ptp90) cc_final: 0.8164 (mpp-170) REVERT: C 34 MET cc_start: 0.8689 (mmm) cc_final: 0.8180 (mmm) REVERT: C 72 ASP cc_start: 0.8073 (m-30) cc_final: 0.7636 (m-30) REVERT: C 100 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.6171 (t0) REVERT: C 100 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7976 (t0) REVERT: C 110 THR cc_start: 0.8498 (m) cc_final: 0.7918 (p) REVERT: E 137 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8204 (p0) REVERT: E 434 MET cc_start: 0.8609 (ttp) cc_final: 0.8037 (ttp) REVERT: G 530 MET cc_start: 0.7465 (mmm) cc_final: 0.6990 (mmm) REVERT: G 535 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7190 (mmt) REVERT: G 542 ARG cc_start: 0.7828 (ttt-90) cc_final: 0.7334 (mtt-85) REVERT: G 601 LYS cc_start: 0.9186 (pttm) cc_final: 0.8696 (pttm) REVERT: G 625 ASN cc_start: 0.8915 (m-40) cc_final: 0.8617 (m110) REVERT: G 649 SER cc_start: 0.8807 (m) cc_final: 0.8526 (p) REVERT: Q 58 VAL cc_start: 0.7472 (t) cc_final: 0.6961 (t) REVERT: O 26 ASN cc_start: 0.7604 (m-40) cc_final: 0.7327 (m110) REVERT: O 68 THR cc_start: 0.9058 (m) cc_final: 0.8647 (p) REVERT: O 72 ASP cc_start: 0.8118 (t0) cc_final: 0.7576 (m-30) REVERT: O 100 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7973 (t0) REVERT: M 39 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7285 (mmtm) REVERT: J 11 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8328 (tp) REVERT: J 38 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7047 (ttm-80) REVERT: J 79 TYR cc_start: 0.8457 (m-80) cc_final: 0.8223 (m-10) REVERT: I 535 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7342 (mmm) REVERT: I 601 LYS cc_start: 0.9317 (pttm) cc_final: 0.8665 (ptpp) REVERT: I 625 ASN cc_start: 0.9041 (m-40) cc_final: 0.8508 (m-40) REVERT: I 651 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7483 (p0) REVERT: R 24 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7881 (tmt170) REVERT: P 68 THR cc_start: 0.9010 (m) cc_final: 0.8616 (p) REVERT: N 42 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8456 (mmmm) REVERT: K 34 MET cc_start: 0.8598 (mmm) cc_final: 0.7810 (mmm) REVERT: K 100 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8033 (t0) REVERT: K 110 THR cc_start: 0.8549 (m) cc_final: 0.8062 (p) outliers start: 106 outliers final: 69 residues processed: 354 average time/residue: 0.1780 time to fit residues: 98.1698 Evaluate side-chains 341 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 257 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 86 TYR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 58 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 257 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 290 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 250 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN R 79 GLN P 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058993 restraints weight = 90970.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061395 restraints weight = 44655.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062977 restraints weight = 29773.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063969 restraints weight = 23437.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064556 restraints weight = 20294.156| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26541 Z= 0.141 Angle : 0.724 9.383 36354 Z= 0.347 Chirality : 0.047 0.319 4602 Planarity : 0.004 0.077 4233 Dihedral : 8.593 59.872 6939 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 2.88 % Allowed : 14.44 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2967 helix: 0.53 (0.28), residues: 363 sheet: 0.30 (0.17), residues: 936 loop : -0.54 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 61 TYR 0.019 0.001 TYR R 49 PHE 0.013 0.002 PHE R 98 TRP 0.054 0.002 TRP D 35 HIS 0.011 0.001 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00316 (26313) covalent geometry : angle 0.69463 (35712) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.23651 ( 84) hydrogen bonds : bond 0.03905 ( 909) hydrogen bonds : angle 5.83110 ( 2421) link_ALPHA1-2 : bond 0.00371 ( 24) link_ALPHA1-2 : angle 1.85192 ( 72) link_ALPHA1-3 : bond 0.00844 ( 30) link_ALPHA1-3 : angle 2.04339 ( 90) link_ALPHA1-6 : bond 0.00987 ( 30) link_ALPHA1-6 : angle 1.91298 ( 90) link_BETA1-4 : bond 0.00358 ( 51) link_BETA1-4 : angle 1.49494 ( 153) link_NAG-ASN : bond 0.00253 ( 51) link_NAG-ASN : angle 1.61499 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 288 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8835 (tpp) cc_final: 0.8082 (tpp) REVERT: A 161 MET cc_start: 0.8806 (tpt) cc_final: 0.8534 (tpt) REVERT: B 535 MET cc_start: 0.7977 (tpt) cc_final: 0.7631 (mmt) REVERT: B 584 GLU cc_start: 0.8669 (tt0) cc_final: 0.8330 (tm-30) REVERT: B 651 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7839 (p0) REVERT: L 78 LEU cc_start: 0.8267 (tp) cc_final: 0.7066 (pp) REVERT: L 79 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7369 (tm-30) REVERT: L 86 TYR cc_start: 0.7412 (m-80) cc_final: 0.7145 (m-80) REVERT: H 68 THR cc_start: 0.9027 (m) cc_final: 0.8659 (p) REVERT: H 72 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: D 23 CYS cc_start: 0.3741 (p) cc_final: 0.2934 (p) REVERT: D 30 GLU cc_start: 0.8939 (mp0) cc_final: 0.8487 (pm20) REVERT: D 42 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8281 (mmmm) REVERT: D 103 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8147 (mpp-170) REVERT: C 11 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8286 (tp) REVERT: C 34 MET cc_start: 0.8734 (mmm) cc_final: 0.8190 (mmm) REVERT: C 72 ASP cc_start: 0.7965 (m-30) cc_final: 0.7560 (m-30) REVERT: C 100 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7816 (t0) REVERT: C 110 THR cc_start: 0.8439 (m) cc_final: 0.7846 (p) REVERT: E 137 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8004 (p0) REVERT: E 434 MET cc_start: 0.8570 (ttp) cc_final: 0.7989 (ttp) REVERT: G 530 MET cc_start: 0.7520 (mmm) cc_final: 0.7032 (mmm) REVERT: G 535 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7100 (mmt) REVERT: G 601 LYS cc_start: 0.9077 (pttm) cc_final: 0.8609 (pttm) REVERT: Q 4 MET cc_start: 0.8291 (ttp) cc_final: 0.7813 (tmm) REVERT: Q 55 LYS cc_start: 0.8027 (tttt) cc_final: 0.7507 (ttmt) REVERT: Q 58 VAL cc_start: 0.7355 (t) cc_final: 0.6883 (t) REVERT: O 26 ASN cc_start: 0.7679 (m-40) cc_final: 0.7436 (m110) REVERT: O 68 THR cc_start: 0.8978 (m) cc_final: 0.8568 (p) REVERT: O 72 ASP cc_start: 0.7988 (t0) cc_final: 0.7463 (m-30) REVERT: M 35 TRP cc_start: 0.5863 (m-10) cc_final: 0.5368 (m-10) REVERT: M 39 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7484 (mmtm) REVERT: M 103 ARG cc_start: 0.8849 (mpp-170) cc_final: 0.7959 (tpp80) REVERT: J 11 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8265 (tp) REVERT: J 79 TYR cc_start: 0.8497 (m-80) cc_final: 0.8224 (m-10) REVERT: J 100 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6153 (t0) REVERT: I 530 MET cc_start: 0.7554 (mmt) cc_final: 0.7299 (mmt) REVERT: I 535 MET cc_start: 0.8029 (tpt) cc_final: 0.7462 (mmm) REVERT: I 601 LYS cc_start: 0.9248 (pttm) cc_final: 0.8621 (ptpp) REVERT: I 625 ASN cc_start: 0.9016 (m-40) cc_final: 0.8499 (m-40) REVERT: I 626 MET cc_start: 0.8248 (tmm) cc_final: 0.7933 (tmm) REVERT: I 651 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7443 (p0) REVERT: R 24 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7342 (ttp80) REVERT: N 42 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8521 (mmmm) REVERT: K 34 MET cc_start: 0.8569 (mmm) cc_final: 0.7789 (mmm) REVERT: K 98 ASP cc_start: 0.8755 (m-30) cc_final: 0.8555 (m-30) REVERT: K 100 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7776 (t0) REVERT: K 107 THR cc_start: 0.7850 (m) cc_final: 0.7562 (m) REVERT: K 110 THR cc_start: 0.8500 (m) cc_final: 0.8001 (p) outliers start: 75 outliers final: 50 residues processed: 342 average time/residue: 0.1716 time to fit residues: 91.3142 Evaluate side-chains 317 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 276 optimal weight: 40.0000 chunk 151 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 82 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN E 195 ASN E 328 GLN Q 89 GLN F 195 ASN P 81 GLN N 89 GLN ** K 100CASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.082051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057004 restraints weight = 91918.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059295 restraints weight = 45982.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060788 restraints weight = 31123.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061733 restraints weight = 24757.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062318 restraints weight = 21568.250| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26541 Z= 0.244 Angle : 0.795 9.110 36354 Z= 0.382 Chirality : 0.048 0.324 4602 Planarity : 0.005 0.078 4233 Dihedral : 8.607 59.475 6939 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 3.34 % Allowed : 14.59 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 2967 helix: 0.32 (0.28), residues: 369 sheet: 0.10 (0.17), residues: 972 loop : -0.65 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 83 TYR 0.017 0.002 TYR Q 49 PHE 0.018 0.002 PHE E 376 TRP 0.048 0.002 TRP D 35 HIS 0.007 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00555 (26313) covalent geometry : angle 0.76165 (35712) SS BOND : bond 0.00428 ( 42) SS BOND : angle 1.39779 ( 84) hydrogen bonds : bond 0.04249 ( 909) hydrogen bonds : angle 5.93434 ( 2421) link_ALPHA1-2 : bond 0.00260 ( 24) link_ALPHA1-2 : angle 2.27958 ( 72) link_ALPHA1-3 : bond 0.00762 ( 30) link_ALPHA1-3 : angle 2.12471 ( 90) link_ALPHA1-6 : bond 0.00839 ( 30) link_ALPHA1-6 : angle 1.96769 ( 90) link_BETA1-4 : bond 0.00424 ( 51) link_BETA1-4 : angle 1.66985 ( 153) link_NAG-ASN : bond 0.00527 ( 51) link_NAG-ASN : angle 1.90298 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 270 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8916 (tpp) cc_final: 0.8251 (tpp) REVERT: B 535 MET cc_start: 0.7842 (tpt) cc_final: 0.7447 (mmt) REVERT: B 584 GLU cc_start: 0.8653 (tt0) cc_final: 0.8356 (tm-30) REVERT: B 601 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8904 (mttt) REVERT: B 651 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7878 (p0) REVERT: L 55 LYS cc_start: 0.7957 (tttt) cc_final: 0.7589 (ptmt) REVERT: L 78 LEU cc_start: 0.8339 (tp) cc_final: 0.7145 (pp) REVERT: L 79 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7368 (tm-30) REVERT: H 68 THR cc_start: 0.8993 (m) cc_final: 0.8637 (p) REVERT: H 72 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: H 79 TYR cc_start: 0.7909 (m-80) cc_final: 0.7415 (m-10) REVERT: H 100 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8570 (t0) REVERT: D 30 GLU cc_start: 0.8811 (mp0) cc_final: 0.8391 (pm20) REVERT: D 42 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8303 (mmmm) REVERT: C 11 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 34 MET cc_start: 0.8706 (mmm) cc_final: 0.8158 (mmm) REVERT: C 72 ASP cc_start: 0.8162 (m-30) cc_final: 0.7534 (m-30) REVERT: C 100 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8018 (t0) REVERT: C 110 THR cc_start: 0.8401 (m) cc_final: 0.7903 (p) REVERT: E 434 MET cc_start: 0.8614 (ttp) cc_final: 0.8006 (ttp) REVERT: G 530 MET cc_start: 0.7268 (mmm) cc_final: 0.6770 (mmm) REVERT: G 535 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7175 (mmt) REVERT: Q 4 MET cc_start: 0.8267 (ttp) cc_final: 0.7894 (tmm) REVERT: Q 55 LYS cc_start: 0.7635 (tttt) cc_final: 0.7416 (ttmt) REVERT: Q 58 VAL cc_start: 0.7428 (t) cc_final: 0.6966 (t) REVERT: Q 61 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6624 (ptm160) REVERT: O 68 THR cc_start: 0.8966 (m) cc_final: 0.8556 (p) REVERT: O 79 TYR cc_start: 0.7656 (m-80) cc_final: 0.7096 (m-80) REVERT: M 39 LYS cc_start: 0.7862 (mmtm) cc_final: 0.6587 (mmtm) REVERT: M 103 ARG cc_start: 0.8915 (mpp-170) cc_final: 0.8008 (tpp80) REVERT: J 11 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8270 (tp) REVERT: J 38 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6694 (ttm-80) REVERT: J 79 TYR cc_start: 0.8499 (m-80) cc_final: 0.8081 (m-10) REVERT: I 530 MET cc_start: 0.7546 (mmt) cc_final: 0.7241 (mmt) REVERT: I 535 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7455 (mmm) REVERT: I 601 LYS cc_start: 0.9324 (pttm) cc_final: 0.8729 (ptpp) REVERT: I 625 ASN cc_start: 0.8915 (m-40) cc_final: 0.8371 (m-40) REVERT: I 651 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7444 (p0) REVERT: R 24 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7415 (ttp80) REVERT: R 105 GLU cc_start: 0.7449 (pp20) cc_final: 0.6874 (tp30) REVERT: N 42 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8391 (mmmm) REVERT: K 34 MET cc_start: 0.8538 (mmm) cc_final: 0.7889 (mmm) REVERT: K 57 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6274 (ttm170) REVERT: K 82 MET cc_start: 0.7755 (mtp) cc_final: 0.7180 (mtt) REVERT: K 100 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8019 (t0) REVERT: K 110 THR cc_start: 0.8553 (m) cc_final: 0.8053 (p) outliers start: 87 outliers final: 56 residues processed: 335 average time/residue: 0.1681 time to fit residues: 88.0498 Evaluate side-chains 325 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 58 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 238 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 121 optimal weight: 0.2980 chunk 108 optimal weight: 8.9990 chunk 290 optimal weight: 0.8980 chunk 226 optimal weight: 0.2980 chunk 140 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN H 3 GLN H 81 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN O 100CASN M 90 HIS F 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.084949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060034 restraints weight = 91182.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062452 restraints weight = 44532.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064053 restraints weight = 29641.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065060 restraints weight = 23255.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065682 restraints weight = 20084.196| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26541 Z= 0.127 Angle : 0.719 11.762 36354 Z= 0.344 Chirality : 0.046 0.317 4602 Planarity : 0.004 0.070 4233 Dihedral : 7.772 59.769 6939 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.12 % Favored : 94.78 % Rotamer: Outliers : 2.04 % Allowed : 15.98 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2967 helix: 0.70 (0.29), residues: 363 sheet: 0.22 (0.17), residues: 975 loop : -0.62 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 99 TYR 0.018 0.001 TYR Q 49 PHE 0.016 0.002 PHE R 98 TRP 0.053 0.002 TRP D 35 HIS 0.005 0.001 HIS O 82A Details of bonding type rmsd covalent geometry : bond 0.00278 (26313) covalent geometry : angle 0.69409 (35712) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.09684 ( 84) hydrogen bonds : bond 0.03755 ( 909) hydrogen bonds : angle 5.68858 ( 2421) link_ALPHA1-2 : bond 0.00455 ( 24) link_ALPHA1-2 : angle 1.70382 ( 72) link_ALPHA1-3 : bond 0.00830 ( 30) link_ALPHA1-3 : angle 1.91374 ( 90) link_ALPHA1-6 : bond 0.00989 ( 30) link_ALPHA1-6 : angle 1.81969 ( 90) link_BETA1-4 : bond 0.00414 ( 51) link_BETA1-4 : angle 1.42947 ( 153) link_NAG-ASN : bond 0.00191 ( 51) link_NAG-ASN : angle 1.46291 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 315 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8795 (tpp) cc_final: 0.8101 (tpp) REVERT: A 161 MET cc_start: 0.8814 (tpt) cc_final: 0.8447 (tpt) REVERT: B 535 MET cc_start: 0.8023 (tpt) cc_final: 0.7751 (mmt) REVERT: B 584 GLU cc_start: 0.8663 (tt0) cc_final: 0.8345 (tm-30) REVERT: B 601 LYS cc_start: 0.9027 (pttt) cc_final: 0.8407 (mptt) REVERT: B 651 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7861 (p0) REVERT: L 55 LYS cc_start: 0.7934 (tttt) cc_final: 0.7602 (ptmt) REVERT: L 78 LEU cc_start: 0.8271 (tp) cc_final: 0.7132 (pp) REVERT: L 79 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7356 (tm-30) REVERT: L 86 TYR cc_start: 0.7344 (m-80) cc_final: 0.7120 (m-80) REVERT: H 68 THR cc_start: 0.8880 (m) cc_final: 0.8547 (p) REVERT: H 79 TYR cc_start: 0.7856 (m-80) cc_final: 0.7380 (m-10) REVERT: D 24 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: D 30 GLU cc_start: 0.8827 (mp0) cc_final: 0.8487 (pm20) REVERT: D 42 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8367 (mmmm) REVERT: D 103 ARG cc_start: 0.8779 (ptp90) cc_final: 0.8122 (tpp80) REVERT: C 11 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8062 (tp) REVERT: C 34 MET cc_start: 0.8704 (mmm) cc_final: 0.8146 (mmm) REVERT: C 110 THR cc_start: 0.8370 (m) cc_final: 0.7763 (p) REVERT: E 434 MET cc_start: 0.8538 (ttp) cc_final: 0.7904 (ttp) REVERT: G 530 MET cc_start: 0.7987 (mmm) cc_final: 0.7574 (mmm) REVERT: G 535 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7578 (mmt) REVERT: G 601 LYS cc_start: 0.9032 (pttm) cc_final: 0.8587 (pttm) REVERT: G 648 GLU cc_start: 0.8918 (tp30) cc_final: 0.8547 (pp20) REVERT: Q 4 MET cc_start: 0.8228 (ttp) cc_final: 0.7883 (tmm) REVERT: Q 55 LYS cc_start: 0.7584 (tttt) cc_final: 0.7302 (ttmt) REVERT: Q 58 VAL cc_start: 0.7480 (t) cc_final: 0.7017 (t) REVERT: M 35 TRP cc_start: 0.5261 (m-10) cc_final: 0.5043 (m-10) REVERT: M 39 LYS cc_start: 0.7279 (mmtm) cc_final: 0.6724 (mmtm) REVERT: M 103 ARG cc_start: 0.8927 (mpp-170) cc_final: 0.8022 (tpp80) REVERT: J 11 LEU cc_start: 0.8454 (mp) cc_final: 0.8234 (tp) REVERT: J 79 TYR cc_start: 0.8542 (m-80) cc_final: 0.8189 (m-10) REVERT: J 82 MET cc_start: 0.7405 (mtm) cc_final: 0.7144 (ptp) REVERT: J 100 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6114 (t0) REVERT: F 95 MET cc_start: 0.8245 (ptm) cc_final: 0.7676 (ptm) REVERT: F 347 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8988 (ttpp) REVERT: I 530 MET cc_start: 0.7542 (mmt) cc_final: 0.7231 (mmt) REVERT: I 535 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7456 (mmm) REVERT: I 601 LYS cc_start: 0.9220 (pttm) cc_final: 0.8623 (ptpp) REVERT: I 625 ASN cc_start: 0.8954 (m-40) cc_final: 0.8529 (t0) REVERT: I 626 MET cc_start: 0.8207 (tmm) cc_final: 0.7845 (tmm) REVERT: I 651 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7436 (p0) REVERT: R 24 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7376 (ttp80) REVERT: R 105 GLU cc_start: 0.7390 (pp20) cc_final: 0.6895 (tm-30) REVERT: P 34 MET cc_start: 0.8484 (mtp) cc_final: 0.8146 (mtp) REVERT: N 4 MET cc_start: 0.3958 (ppp) cc_final: 0.3736 (ppp) REVERT: N 42 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8391 (mmmm) REVERT: K 34 MET cc_start: 0.8505 (mmm) cc_final: 0.7871 (mmm) REVERT: K 57 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6607 (ttm170) REVERT: K 82 MET cc_start: 0.7693 (mtp) cc_final: 0.7258 (mtt) REVERT: K 100 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7745 (t0) REVERT: K 110 THR cc_start: 0.8426 (m) cc_final: 0.7923 (p) outliers start: 53 outliers final: 32 residues processed: 351 average time/residue: 0.1830 time to fit residues: 99.3798 Evaluate side-chains 316 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 4.9990 chunk 123 optimal weight: 0.0060 chunk 188 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 69 optimal weight: 0.0670 chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 272 optimal weight: 5.9990 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN E 195 ASN F 195 ASN P 82AHIS N 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060916 restraints weight = 90641.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063354 restraints weight = 44286.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064972 restraints weight = 29442.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065995 restraints weight = 23078.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066567 restraints weight = 19893.915| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26541 Z= 0.125 Angle : 0.715 11.393 36354 Z= 0.345 Chirality : 0.046 0.313 4602 Planarity : 0.004 0.064 4233 Dihedral : 7.315 58.388 6939 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 1.54 % Allowed : 16.86 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 2967 helix: 0.73 (0.29), residues: 366 sheet: 0.18 (0.16), residues: 1038 loop : -0.71 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 83 TYR 0.018 0.001 TYR Q 49 PHE 0.013 0.001 PHE R 98 TRP 0.055 0.002 TRP D 35 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00277 (26313) covalent geometry : angle 0.69194 (35712) SS BOND : bond 0.00237 ( 42) SS BOND : angle 0.98267 ( 84) hydrogen bonds : bond 0.03725 ( 909) hydrogen bonds : angle 5.53395 ( 2421) link_ALPHA1-2 : bond 0.00460 ( 24) link_ALPHA1-2 : angle 1.66817 ( 72) link_ALPHA1-3 : bond 0.00799 ( 30) link_ALPHA1-3 : angle 1.85950 ( 90) link_ALPHA1-6 : bond 0.00979 ( 30) link_ALPHA1-6 : angle 1.74238 ( 90) link_BETA1-4 : bond 0.00423 ( 51) link_BETA1-4 : angle 1.48205 ( 153) link_NAG-ASN : bond 0.00166 ( 51) link_NAG-ASN : angle 1.40447 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8809 (tpp) cc_final: 0.8168 (tpp) REVERT: B 584 GLU cc_start: 0.8656 (tt0) cc_final: 0.8336 (tm-30) REVERT: B 601 LYS cc_start: 0.9047 (pttt) cc_final: 0.8334 (mptt) REVERT: B 651 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7891 (p0) REVERT: L 55 LYS cc_start: 0.7781 (tttt) cc_final: 0.7156 (ptmt) REVERT: L 78 LEU cc_start: 0.8090 (tp) cc_final: 0.6920 (pp) REVERT: L 79 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7439 (tm-30) REVERT: L 86 TYR cc_start: 0.7395 (m-80) cc_final: 0.7160 (m-80) REVERT: H 79 TYR cc_start: 0.8003 (m-80) cc_final: 0.7576 (m-10) REVERT: D 30 GLU cc_start: 0.8852 (mp0) cc_final: 0.8536 (pm20) REVERT: D 42 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8420 (mmmm) REVERT: D 103 ARG cc_start: 0.8777 (ptp90) cc_final: 0.8145 (tpp80) REVERT: C 34 MET cc_start: 0.8681 (mmm) cc_final: 0.8162 (mmm) REVERT: E 434 MET cc_start: 0.8507 (ttp) cc_final: 0.7958 (ttp) REVERT: G 530 MET cc_start: 0.7552 (mmm) cc_final: 0.7230 (mmm) REVERT: G 535 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7501 (mmt) REVERT: G 601 LYS cc_start: 0.9069 (pttm) cc_final: 0.8218 (mptt) REVERT: G 648 GLU cc_start: 0.8903 (tp30) cc_final: 0.8522 (pp20) REVERT: Q 4 MET cc_start: 0.8188 (ttp) cc_final: 0.7841 (tmm) REVERT: Q 55 LYS cc_start: 0.7560 (tttt) cc_final: 0.7293 (ttmt) REVERT: Q 58 VAL cc_start: 0.7498 (t) cc_final: 0.7033 (t) REVERT: O 68 THR cc_start: 0.8879 (m) cc_final: 0.8595 (p) REVERT: O 72 ASP cc_start: 0.7775 (t0) cc_final: 0.6927 (m-30) REVERT: M 4 MET cc_start: 0.3524 (ttm) cc_final: 0.2999 (ppp) REVERT: M 35 TRP cc_start: 0.5299 (m-10) cc_final: 0.5028 (m-10) REVERT: M 39 LYS cc_start: 0.7504 (mmtm) cc_final: 0.7125 (mmtm) REVERT: M 103 ARG cc_start: 0.9029 (mpp-170) cc_final: 0.8171 (tpp80) REVERT: J 57 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7399 (ttm-80) REVERT: J 82 MET cc_start: 0.7358 (mtm) cc_final: 0.7024 (mtp) REVERT: F 95 MET cc_start: 0.8266 (ptm) cc_final: 0.7714 (ptm) REVERT: I 535 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7776 (mmt) REVERT: I 601 LYS cc_start: 0.9205 (pttm) cc_final: 0.8613 (ptpp) REVERT: I 651 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7562 (p0) REVERT: R 4 MET cc_start: 0.8157 (ttp) cc_final: 0.7871 (tmm) REVERT: R 24 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7526 (ttp80) REVERT: R 105 GLU cc_start: 0.7275 (pp20) cc_final: 0.6818 (tm-30) REVERT: N 42 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8393 (mmmm) REVERT: N 103 ARG cc_start: 0.8764 (ptp90) cc_final: 0.8167 (tpp80) REVERT: K 34 MET cc_start: 0.8522 (mmm) cc_final: 0.7874 (mmm) REVERT: K 57 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6997 (ttm170) REVERT: K 110 THR cc_start: 0.8392 (m) cc_final: 0.7894 (p) outliers start: 40 outliers final: 27 residues processed: 329 average time/residue: 0.1858 time to fit residues: 95.0680 Evaluate side-chains 310 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 57 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 0.3980 chunk 182 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 277 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 265 optimal weight: 0.0970 chunk 96 optimal weight: 9.9990 overall best weight: 2.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 81 GLN E 195 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN F 348 GLN P 82AHIS K 100CASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.083195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058241 restraints weight = 91062.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060556 restraints weight = 45355.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.062084 restraints weight = 30552.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063004 restraints weight = 24195.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063625 restraints weight = 21065.947| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26541 Z= 0.198 Angle : 0.772 11.559 36354 Z= 0.369 Chirality : 0.047 0.310 4602 Planarity : 0.005 0.072 4233 Dihedral : 7.245 59.738 6939 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 2.15 % Allowed : 16.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2967 helix: 0.70 (0.29), residues: 363 sheet: 0.08 (0.16), residues: 1032 loop : -0.75 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 99 TYR 0.017 0.002 TYR Q 49 PHE 0.014 0.002 PHE O 27 TRP 0.064 0.002 TRP D 35 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00461 (26313) covalent geometry : angle 0.74495 (35712) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.12124 ( 84) hydrogen bonds : bond 0.04028 ( 909) hydrogen bonds : angle 5.66172 ( 2421) link_ALPHA1-2 : bond 0.00219 ( 24) link_ALPHA1-2 : angle 2.00200 ( 72) link_ALPHA1-3 : bond 0.00697 ( 30) link_ALPHA1-3 : angle 1.91285 ( 90) link_ALPHA1-6 : bond 0.00829 ( 30) link_ALPHA1-6 : angle 1.80436 ( 90) link_BETA1-4 : bond 0.00396 ( 51) link_BETA1-4 : angle 1.62523 ( 153) link_NAG-ASN : bond 0.00388 ( 51) link_NAG-ASN : angle 1.68949 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.98 seconds wall clock time: 80 minutes 53.09 seconds (4853.09 seconds total)