Starting phenix.real_space_refine on Fri Feb 6 15:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.map" model { file = "/net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogu_70476/02_2026/9ogu_70476.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 135 5.16 5 C 16063 2.51 5 N 4308 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25622 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3423 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 986 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 982 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3463 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "C" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3440 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "M" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "O" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "P" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "Q" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "R" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1038 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} 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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} 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 Time building chain proxies: 5.41, per 1000 atoms: 0.21 Number of scatterers: 25622 At special positions: 0 Unit cell: (153.7, 149.35, 156.6, 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 135 16.00 O 5116 8.00 N 4308 7.00 C 16063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS C 501 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 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=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 100 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 5 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 4 " " BMA o 3 " - " MAN o 7 " " BMA r 3 " - " MAN r 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG 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 h 1 " - " NAG h 2 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " BMA m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 88 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 363 " " NAG X 1 " - " ASN A 386 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 137 " " NAG a 1 " - " ASN E 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 363 " " NAG g 1 " - " ASN E 386 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 137 " " NAG j 1 " - " ASN C 156 " " NAG k 1 " - " ASN C 262 " " NAG l 1 " - " ASN C 276 " " NAG m 1 " - " ASN C 295 " " NAG n 1 " - " ASN C 301 " " NAG o 1 " - " ASN C 332 " " NAG p 1 " - " ASN C 363 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 137 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 766.7 milliseconds 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5636 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 65 sheets defined 16.6% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.256A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.697A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.986A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.231A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.077A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.253A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 4.070A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.183A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.946A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.686A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 623' Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.781A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.397A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.709A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.246A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.573A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.921A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.133A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.909A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.704A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.661A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.767A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.788A pdb=" N THR H 95 " --> pdb=" O SER H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.600A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.583A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.829A pdb=" N ASP M 31 " --> pdb=" O ASN M 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 76 through 79 removed outlier: 4.391A pdb=" N ASP M 79 " --> pdb=" O TRP M 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.530A pdb=" N SER N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.622A pdb=" N GLU O 83 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.513A pdb=" N TYR P 32 " --> pdb=" O ILE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 95 removed outlier: 3.890A pdb=" N THR P 95 " --> pdb=" O SER P 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.705A pdb=" N ASP R 31 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN R 32 " --> pdb=" O VAL R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.119A pdb=" N GLU S 83 " --> pdb=" O ALA S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.888A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.638A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.166A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.177A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.680A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.132A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.680A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.177A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.960A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.509A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 603 through 609 removed outlier: 4.713A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AB6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.273A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.017A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.205A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.017A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 303 through 312 removed outlier: 3.998A pdb=" N ASP E 322 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.050A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.190A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.093A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.188A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 274 removed outlier: 7.188A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.745A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.727A pdb=" N PHE H 83 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.852A pdb=" N ALA H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE H 33 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.510A pdb=" N GLU I 70 " --> pdb=" O TRP I 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.594A pdb=" N LEU I 11 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.594A pdb=" N LEU I 11 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 62 through 63 Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.651A pdb=" N VAL J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.651A pdb=" N VAL J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 100 through 100A removed outlier: 3.524A pdb=" N PHE J 100K" --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 6 through 13 Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 23 removed outlier: 4.174A pdb=" N ALA K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 44 through 48 removed outlier: 5.461A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.887A pdb=" N ALA M 10 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.887A pdb=" N ALA M 10 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 112 " --> pdb=" O ARG M 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AF1, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.856A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.856A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL N 102 " --> pdb=" O THR N 94 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS N 96 " --> pdb=" O MET N 100P" (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET N 100P" --> pdb=" O LYS N 96 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 100 through 100A Processing sheet with id=AF7, first strand: chain 'O' and resid 6 through 13 removed outlier: 6.799A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU O 100 " --> pdb=" O CYS O 88 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N CYS O 88 " --> pdb=" O GLU O 100 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE O 48 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AF9, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.537A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 10 through 11 removed outlier: 4.477A pdb=" N VAL P 112 " --> pdb=" O ARG P 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AG4, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.937A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.937A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 19 through 20 removed outlier: 4.004A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE Q 75 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'R' and resid 57 through 59 removed outlier: 5.376A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR R 33 " --> pdb=" O THR R 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE R 89 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 99 through 100A Processing sheet with id=AH1, first strand: chain 'S' and resid 6 through 13 removed outlier: 3.828A pdb=" N VAL S 13 " --> pdb=" O ILE S 105 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 19 through 26 removed outlier: 3.609A pdb=" N ALA S 71 " --> pdb=" O CYS S 23 " (cutoff:3.500A) 899 hydrogen bonds defined for protein. 2316 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: 4.94 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7908 1.34 - 1.47: 7053 1.47 - 1.60: 11044 1.60 - 1.73: 1 1.73 - 1.86: 179 Bond restraints: 26185 Sorted by residual: bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.700 0.108 3.30e-02 9.18e+02 1.07e+01 bond pdb=" CB ASN A 363 " pdb=" CG ASN A 363 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.52e+00 bond pdb=" C SER Q 7 " pdb=" N PRO Q 8 " ideal model delta sigma weight residual 1.332 1.357 -0.026 1.30e-02 5.92e+03 3.85e+00 bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.30e+00 bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 ... (remaining 26180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 35057 3.52 - 7.04: 463 7.04 - 10.56: 60 10.56 - 14.08: 5 14.08 - 17.60: 10 Bond angle restraints: 35595 Sorted by residual: angle pdb=" C ASN E 339 " pdb=" N GLU E 340 " pdb=" CA GLU E 340 " ideal model delta sigma weight residual 121.54 136.62 -15.08 1.91e+00 2.74e-01 6.24e+01 angle pdb=" CA CYS C 501 " pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " ideal model delta sigma weight residual 114.40 129.24 -14.84 2.30e+00 1.89e-01 4.16e+01 angle pdb=" C ASN A 339 " pdb=" N GLU A 340 " pdb=" CA GLU A 340 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C2 NAG C 607 " pdb=" N2 NAG C 607 " pdb=" C7 NAG C 607 " ideal model delta sigma weight residual 124.56 139.81 -15.25 3.00e+00 1.11e-01 2.58e+01 angle pdb=" CA LEU N 63 " pdb=" CB LEU N 63 " pdb=" CG LEU N 63 " ideal model delta sigma weight residual 116.30 133.90 -17.60 3.50e+00 8.16e-02 2.53e+01 ... (remaining 35590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 15522 24.57 - 49.13: 1180 49.13 - 73.70: 254 73.70 - 98.26: 54 98.26 - 122.83: 23 Dihedral angle restraints: 17033 sinusoidal: 8265 harmonic: 8768 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.08 55.08 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CA ALA C 204 " pdb=" C ALA C 204 " pdb=" N CYS C 205 " pdb=" CA CYS C 205 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 17030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4161 0.149 - 0.298: 102 0.298 - 0.447: 7 0.447 - 0.597: 1 0.597 - 0.746: 2 Chirality restraints: 4273 Sorted by residual: chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 363 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE E 294 " pdb=" CA ILE E 294 " pdb=" CG1 ILE E 294 " pdb=" CG2 ILE E 294 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 4270 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 304 " -0.432 9.50e-02 1.11e+02 1.95e-01 2.88e+01 pdb=" NE ARG C 304 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 304 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG C 304 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 304 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 77 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ASN Q 77 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN Q 77 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU Q 78 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 40 " 0.244 9.50e-02 1.11e+02 1.10e-01 9.55e+00 pdb=" NE ARG L 40 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG L 40 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG L 40 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG L 40 " 0.000 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 7093 2.83 - 3.35: 21903 3.35 - 3.87: 41908 3.87 - 4.38: 48647 4.38 - 4.90: 85365 Nonbonded interactions: 204916 Sorted by model distance: nonbonded pdb=" O5 NAG g 1 " pdb=" O6 NAG g 1 " model vdw 2.316 2.432 nonbonded pdb=" O4 NAG l 2 " pdb=" O2 BMA l 3 " model vdw 2.334 2.432 nonbonded pdb=" O5 MAN o 5 " pdb=" O6 MAN o 5 " model vdw 2.385 2.432 nonbonded pdb=" O5 MAN e 6 " pdb=" O6 MAN e 6 " model vdw 2.388 2.432 nonbonded pdb=" O5 MAN Z 4 " pdb=" O6 MAN Z 4 " model vdw 2.398 2.432 ... (remaining 204911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 608) selection = (chain 'C' and (resid 33 through 184 or resid 189 through 608)) selection = (chain 'E' and (resid 33 through 138 or resid 150 through 184 or resid 189 throu \ gh 608)) } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 572 through 701)) selection = (chain 'D' and (resid 520 through 546 or resid 568 or resid 573 through 701)) selection = (chain 'F' and (resid 520 through 546 or resid 572 through 701)) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'q' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = (chain 'J' and resid 2 through 112) selection = (chain 'N' and resid 2 through 112) selection = (chain 'R' and resid 2 through 112) } ncs_group { reference = (chain 'K' and resid 5 through 106A) selection = (chain 'O' and resid 5 through 106A) selection = chain 'S' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = (chain 'V' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 2 or resid 5 through 7)) selection = (chain 'o' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'i' selection = chain 'r' } ncs_group { reference = chain 'c' selection = chain 'd' selection = chain 'l' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.570 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 26347 Z= 0.247 Angle : 1.124 19.175 36035 Z= 0.549 Chirality : 0.063 0.746 4273 Planarity : 0.008 0.195 4380 Dihedral : 18.211 122.827 11259 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.83 % Allowed : 22.06 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.93 (0.15), residues: 2986 helix: 0.68 (0.27), residues: 421 sheet: -0.94 (0.16), residues: 912 loop : -0.69 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.002 ARG C 304 TYR 0.026 0.002 TYR R 33 PHE 0.031 0.002 PHE C 159 TRP 0.038 0.002 TRP R 103 HIS 0.012 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00530 (26185) covalent geometry : angle 1.06435 (35595) SS BOND : bond 0.00709 ( 46) SS BOND : angle 2.30586 ( 92) hydrogen bonds : bond 0.14669 ( 844) hydrogen bonds : angle 6.83623 ( 2316) link_ALPHA1-2 : bond 0.00578 ( 5) link_ALPHA1-2 : angle 1.63168 ( 15) link_ALPHA1-3 : bond 0.01122 ( 8) link_ALPHA1-3 : angle 1.85110 ( 24) link_ALPHA1-6 : bond 0.01051 ( 9) link_ALPHA1-6 : angle 1.65219 ( 27) link_BETA1-4 : bond 0.01293 ( 40) link_BETA1-4 : angle 3.46988 ( 120) link_NAG-ASN : bond 0.00754 ( 54) link_NAG-ASN : angle 4.36177 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 477 time to evaluate : 0.776 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: A 46 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7421 (pttp) REVERT: A 117 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8382 (ttpt) REVERT: A 246 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7559 (tp40) REVERT: A 500 ARG cc_start: 0.7750 (ptp-110) cc_final: 0.7489 (mtm110) REVERT: F 542 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7722 (mtm-85) REVERT: D 588 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7439 (mtt90) REVERT: D 618 ASN cc_start: 0.8132 (m-40) cc_final: 0.7354 (p0) REVERT: B 535 MET cc_start: 0.8716 (mpt) cc_final: 0.8266 (mmt) REVERT: B 543 ASN cc_start: 0.8318 (m-40) cc_final: 0.8059 (m110) REVERT: E 99 ASN cc_start: 0.8721 (t0) cc_final: 0.8403 (t0) REVERT: E 110 SER cc_start: 0.8824 (t) cc_final: 0.8340 (m) REVERT: E 490 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8490 (ttpp) REVERT: C 92 GLU cc_start: 0.7621 (tt0) cc_final: 0.7346 (tm-30) REVERT: C 99 ASN cc_start: 0.8555 (t0) cc_final: 0.8086 (t0) REVERT: C 103 GLN cc_start: 0.7956 (mt0) cc_final: 0.7634 (mt0) REVERT: C 106 THR cc_start: 0.8853 (m) cc_final: 0.8484 (p) REVERT: C 168 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8458 (mtpp) REVERT: H 46 GLN cc_start: 0.8224 (tt0) cc_final: 0.7739 (tt0) REVERT: I 36 TYR cc_start: 0.8397 (m-80) cc_final: 0.8047 (m-80) REVERT: I 45 LYS cc_start: 0.8345 (tttm) cc_final: 0.7975 (tttm) REVERT: M 12 THR cc_start: 0.8209 (t) cc_final: 0.7937 (p) REVERT: L 3 GLN cc_start: 0.7550 (mp10) cc_final: 0.7296 (mp10) REVERT: N 96 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8415 (mmtm) REVERT: P 54 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8966 (mttt) REVERT: P 106 ASP cc_start: 0.8551 (m-30) cc_final: 0.8173 (t0) REVERT: Q 50 ASP cc_start: 0.7934 (t0) cc_final: 0.7504 (t0) REVERT: Q 53 LYS cc_start: 0.7529 (mtmm) cc_final: 0.7326 (mttm) REVERT: S 37 GLN cc_start: 0.7069 (tt0) cc_final: 0.6820 (tt0) REVERT: S 42 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: S 54 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6605 (mtm110) outliers start: 22 outliers final: 10 residues processed: 492 average time/residue: 0.1836 time to fit residues: 135.5719 Evaluate side-chains 413 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 400 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 54 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN B 607 ASN E 195 ASN E 428 GLN I 3 GLN M 46 GLN Q 69 GLN R 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118086 restraints weight = 33937.066| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.61 r_work: 0.3195 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26347 Z= 0.131 Angle : 0.738 18.524 36035 Z= 0.332 Chirality : 0.051 0.813 4273 Planarity : 0.004 0.058 4380 Dihedral : 12.783 119.175 5685 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.23 % Allowed : 21.80 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.59 (0.15), residues: 2986 helix: 0.96 (0.27), residues: 423 sheet: -0.61 (0.16), residues: 960 loop : -0.53 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.019 0.001 TYR R 33 PHE 0.014 0.001 PHE H 64 TRP 0.018 0.001 TRP P 50 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00285 (26185) covalent geometry : angle 0.66388 (35595) SS BOND : bond 0.00664 ( 46) SS BOND : angle 1.67813 ( 92) hydrogen bonds : bond 0.03822 ( 844) hydrogen bonds : angle 5.62493 ( 2316) link_ALPHA1-2 : bond 0.00426 ( 5) link_ALPHA1-2 : angle 1.72999 ( 15) link_ALPHA1-3 : bond 0.01072 ( 8) link_ALPHA1-3 : angle 1.48124 ( 24) link_ALPHA1-6 : bond 0.01143 ( 9) link_ALPHA1-6 : angle 2.06097 ( 27) link_BETA1-4 : bond 0.00805 ( 40) link_BETA1-4 : angle 2.93647 ( 120) link_NAG-ASN : bond 0.00593 ( 54) link_NAG-ASN : angle 3.87821 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 414 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7415 (pttp) REVERT: A 117 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8227 (ttpt) REVERT: A 164 GLU cc_start: 0.7495 (pm20) cc_final: 0.7222 (pm20) REVERT: A 246 GLN cc_start: 0.8228 (pt0) cc_final: 0.7577 (tp40) REVERT: A 500 ARG cc_start: 0.7948 (ptp-110) cc_final: 0.7617 (mtm110) REVERT: F 542 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7697 (mtm-85) REVERT: D 535 MET cc_start: 0.8023 (mpp) cc_final: 0.7814 (mpp) REVERT: B 535 MET cc_start: 0.8720 (mpt) cc_final: 0.8190 (mmt) REVERT: B 543 ASN cc_start: 0.8452 (m-40) cc_final: 0.8126 (m110) REVERT: B 581 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8088 (tt) REVERT: E 99 ASN cc_start: 0.8722 (t0) cc_final: 0.8332 (t0) REVERT: E 110 SER cc_start: 0.8823 (t) cc_final: 0.8389 (m) REVERT: E 490 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8450 (ttmt) REVERT: C 66 HIS cc_start: 0.5457 (OUTLIER) cc_final: 0.5162 (t-90) REVERT: C 92 GLU cc_start: 0.7888 (tt0) cc_final: 0.7456 (tm-30) REVERT: C 99 ASN cc_start: 0.8597 (t0) cc_final: 0.8176 (t0) REVERT: C 168 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8526 (mtpp) REVERT: H 13 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7554 (mmtt) REVERT: H 46 GLN cc_start: 0.8334 (tt0) cc_final: 0.7878 (tt0) REVERT: I 45 LYS cc_start: 0.8254 (tttm) cc_final: 0.7866 (ttpm) REVERT: I 65 ARG cc_start: 0.6250 (ttp80) cc_final: 0.6011 (ttp80) REVERT: I 86 TYR cc_start: 0.7456 (m-80) cc_final: 0.7186 (m-80) REVERT: K 13 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6811 (p) REVERT: M 12 THR cc_start: 0.8274 (t) cc_final: 0.8010 (p) REVERT: M 43 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: L 3 GLN cc_start: 0.7604 (mp10) cc_final: 0.7206 (mp10) REVERT: L 79 GLN cc_start: 0.6954 (mp10) cc_final: 0.6751 (mp10) REVERT: L 85 THR cc_start: 0.7109 (m) cc_final: 0.6628 (p) REVERT: O 95 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7833 (t0) REVERT: P 106 ASP cc_start: 0.8552 (m-30) cc_final: 0.8134 (t0) REVERT: Q 53 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7339 (mttm) REVERT: R 33 TYR cc_start: 0.7790 (m-80) cc_final: 0.7449 (m-80) REVERT: R 59 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7478 (m-80) outliers start: 86 outliers final: 55 residues processed: 462 average time/residue: 0.1938 time to fit residues: 135.5393 Evaluate side-chains 459 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 398 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 4 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 161 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN J 58 ASN R 39 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116735 restraints weight = 33838.576| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.77 r_work: 0.3181 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26347 Z= 0.124 Angle : 0.700 18.113 36035 Z= 0.313 Chirality : 0.049 0.857 4273 Planarity : 0.004 0.058 4380 Dihedral : 11.278 112.030 5672 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.94 % Allowed : 21.76 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.39 (0.15), residues: 2986 helix: 1.37 (0.28), residues: 408 sheet: -0.42 (0.16), residues: 952 loop : -0.50 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 56 TYR 0.023 0.001 TYR R 91 PHE 0.018 0.001 PHE H 64 TRP 0.018 0.001 TRP P 50 HIS 0.003 0.000 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00272 (26185) covalent geometry : angle 0.63306 (35595) SS BOND : bond 0.00550 ( 46) SS BOND : angle 1.52256 ( 92) hydrogen bonds : bond 0.03485 ( 844) hydrogen bonds : angle 5.28921 ( 2316) link_ALPHA1-2 : bond 0.00442 ( 5) link_ALPHA1-2 : angle 1.61988 ( 15) link_ALPHA1-3 : bond 0.01125 ( 8) link_ALPHA1-3 : angle 1.56235 ( 24) link_ALPHA1-6 : bond 0.01368 ( 9) link_ALPHA1-6 : angle 2.27762 ( 27) link_BETA1-4 : bond 0.00765 ( 40) link_BETA1-4 : angle 2.73279 ( 120) link_NAG-ASN : bond 0.00474 ( 54) link_NAG-ASN : angle 3.56879 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 406 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7398 (pttp) REVERT: A 117 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8089 (ttpt) REVERT: A 164 GLU cc_start: 0.7608 (pm20) cc_final: 0.7292 (pm20) REVERT: A 246 GLN cc_start: 0.8203 (pt0) cc_final: 0.7479 (tp40) REVERT: A 500 ARG cc_start: 0.7954 (ptp-110) cc_final: 0.7610 (mtm110) REVERT: D 535 MET cc_start: 0.8118 (mpp) cc_final: 0.7892 (mpp) REVERT: B 535 MET cc_start: 0.8734 (mpt) cc_final: 0.8170 (mmt) REVERT: B 543 ASN cc_start: 0.8427 (m-40) cc_final: 0.8080 (m110) REVERT: B 581 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8070 (tt) REVERT: E 110 SER cc_start: 0.8734 (t) cc_final: 0.8283 (m) REVERT: E 117 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7992 (ttpp) REVERT: E 490 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8504 (ttmt) REVERT: C 66 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4989 (t-90) REVERT: C 92 GLU cc_start: 0.7822 (tt0) cc_final: 0.7474 (tm-30) REVERT: C 99 ASN cc_start: 0.8590 (t0) cc_final: 0.8172 (t0) REVERT: C 103 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: H 13 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7590 (mmtt) REVERT: H 109 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8843 (p0) REVERT: I 36 TYR cc_start: 0.8273 (m-80) cc_final: 0.7826 (m-80) REVERT: I 45 LYS cc_start: 0.8263 (tttm) cc_final: 0.7836 (ttpm) REVERT: J 100 TYR cc_start: 0.8476 (p90) cc_final: 0.8230 (p90) REVERT: K 90 ILE cc_start: 0.8722 (mt) cc_final: 0.8314 (mt) REVERT: M 12 THR cc_start: 0.8254 (t) cc_final: 0.7991 (p) REVERT: M 43 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: L 3 GLN cc_start: 0.7498 (mp10) cc_final: 0.7293 (mp10) REVERT: L 79 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: L 85 THR cc_start: 0.7164 (m) cc_final: 0.6765 (p) REVERT: P 106 ASP cc_start: 0.8539 (m-30) cc_final: 0.8065 (t0) REVERT: P 109 ASP cc_start: 0.8972 (p0) cc_final: 0.8721 (p0) REVERT: Q 53 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7343 (mttm) REVERT: R 33 TYR cc_start: 0.7854 (m-80) cc_final: 0.7494 (m-80) REVERT: S 83 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6401 (pm20) outliers start: 105 outliers final: 63 residues processed: 472 average time/residue: 0.1862 time to fit residues: 134.1585 Evaluate side-chains 458 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 227 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN E 195 ASN K 52 ASN M 3 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116060 restraints weight = 33589.025| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.71 r_work: 0.3166 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26347 Z= 0.127 Angle : 0.698 19.676 36035 Z= 0.311 Chirality : 0.049 0.990 4273 Planarity : 0.004 0.055 4380 Dihedral : 10.760 105.436 5670 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.47 % Allowed : 21.58 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 2986 helix: 1.35 (0.28), residues: 415 sheet: -0.38 (0.16), residues: 969 loop : -0.45 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.018 0.001 TYR R 33 PHE 0.022 0.001 PHE H 64 TRP 0.017 0.001 TRP P 50 HIS 0.003 0.000 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00284 (26185) covalent geometry : angle 0.62852 (35595) SS BOND : bond 0.00566 ( 46) SS BOND : angle 1.68088 ( 92) hydrogen bonds : bond 0.03397 ( 844) hydrogen bonds : angle 5.20382 ( 2316) link_ALPHA1-2 : bond 0.00424 ( 5) link_ALPHA1-2 : angle 1.63089 ( 15) link_ALPHA1-3 : bond 0.01129 ( 8) link_ALPHA1-3 : angle 1.57828 ( 24) link_ALPHA1-6 : bond 0.01506 ( 9) link_ALPHA1-6 : angle 2.36339 ( 27) link_BETA1-4 : bond 0.00731 ( 40) link_BETA1-4 : angle 2.70084 ( 120) link_NAG-ASN : bond 0.00592 ( 54) link_NAG-ASN : angle 3.61603 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 397 time to evaluate : 0.862 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 46 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7398 (pttp) REVERT: A 117 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8059 (ttpt) REVERT: A 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.7344 (pm20) REVERT: A 246 GLN cc_start: 0.8210 (pt0) cc_final: 0.7434 (tp40) REVERT: A 500 ARG cc_start: 0.7972 (ptp-110) cc_final: 0.7617 (mtm110) REVERT: F 542 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7518 (mtm-85) REVERT: D 535 MET cc_start: 0.8146 (mpp) cc_final: 0.7906 (mpp) REVERT: B 535 MET cc_start: 0.8744 (mpt) cc_final: 0.8166 (mmt) REVERT: B 543 ASN cc_start: 0.8430 (m-40) cc_final: 0.8073 (m110) REVERT: B 581 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8095 (tt) REVERT: E 110 SER cc_start: 0.8740 (t) cc_final: 0.8318 (m) REVERT: E 117 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7980 (ttpp) REVERT: E 490 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8523 (ttmt) REVERT: C 66 HIS cc_start: 0.5266 (OUTLIER) cc_final: 0.4964 (t-90) REVERT: C 92 GLU cc_start: 0.7816 (tt0) cc_final: 0.7383 (tm-30) REVERT: C 99 ASN cc_start: 0.8606 (t0) cc_final: 0.8183 (t0) REVERT: C 103 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: H 13 LYS cc_start: 0.8387 (mmtp) cc_final: 0.7586 (mmtt) REVERT: H 109 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8857 (p0) REVERT: M 12 THR cc_start: 0.8261 (t) cc_final: 0.8006 (p) REVERT: M 43 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: L 3 GLN cc_start: 0.7603 (mp10) cc_final: 0.7320 (mp10) REVERT: L 79 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: L 85 THR cc_start: 0.7197 (m) cc_final: 0.6752 (p) REVERT: P 106 ASP cc_start: 0.8548 (m-30) cc_final: 0.8059 (t0) REVERT: Q 53 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7385 (mttm) REVERT: R 33 TYR cc_start: 0.7814 (m-80) cc_final: 0.7520 (m-80) REVERT: R 59 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: S 83 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6321 (pm20) outliers start: 119 outliers final: 80 residues processed: 476 average time/residue: 0.1916 time to fit residues: 139.4222 Evaluate side-chains 478 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 389 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 204 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 540 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN J 58 ASN M 3 GLN N 39 GLN O 38 GLN Q 72 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113738 restraints weight = 33615.473| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.66 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 26347 Z= 0.169 Angle : 0.721 21.643 36035 Z= 0.324 Chirality : 0.051 1.121 4273 Planarity : 0.004 0.057 4380 Dihedral : 10.408 105.020 5667 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.65 % Allowed : 21.95 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 2986 helix: 1.26 (0.27), residues: 416 sheet: -0.40 (0.16), residues: 976 loop : -0.45 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.016 0.001 TYR R 33 PHE 0.021 0.002 PHE H 64 TRP 0.018 0.001 TRP P 50 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00395 (26185) covalent geometry : angle 0.64592 (35595) SS BOND : bond 0.00608 ( 46) SS BOND : angle 1.94244 ( 92) hydrogen bonds : bond 0.03578 ( 844) hydrogen bonds : angle 5.20924 ( 2316) link_ALPHA1-2 : bond 0.00333 ( 5) link_ALPHA1-2 : angle 1.78460 ( 15) link_ALPHA1-3 : bond 0.01036 ( 8) link_ALPHA1-3 : angle 1.65438 ( 24) link_ALPHA1-6 : bond 0.01498 ( 9) link_ALPHA1-6 : angle 2.36165 ( 27) link_BETA1-4 : bond 0.00720 ( 40) link_BETA1-4 : angle 2.76534 ( 120) link_NAG-ASN : bond 0.00522 ( 54) link_NAG-ASN : angle 3.79831 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 402 time to evaluate : 0.857 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: A 46 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7410 (pttp) REVERT: A 117 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8074 (ttpt) REVERT: A 164 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 246 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7438 (tp40) REVERT: A 500 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7620 (mtm110) REVERT: F 542 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7574 (mtm-85) REVERT: D 535 MET cc_start: 0.8140 (mpp) cc_final: 0.7906 (mpp) REVERT: B 543 ASN cc_start: 0.8481 (m-40) cc_final: 0.8149 (m110) REVERT: E 110 SER cc_start: 0.8788 (t) cc_final: 0.8350 (m) REVERT: E 490 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8567 (ttmt) REVERT: C 66 HIS cc_start: 0.5275 (OUTLIER) cc_final: 0.4993 (t-90) REVERT: C 92 GLU cc_start: 0.7862 (tt0) cc_final: 0.7399 (tm-30) REVERT: C 99 ASN cc_start: 0.8638 (t0) cc_final: 0.8254 (t0) REVERT: C 103 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: C 434 MET cc_start: 0.9204 (ttp) cc_final: 0.8989 (ttt) REVERT: H 13 LYS cc_start: 0.8379 (mmtp) cc_final: 0.7575 (mmtt) REVERT: H 30 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7947 (mtt180) REVERT: I 45 LYS cc_start: 0.8368 (tttm) cc_final: 0.7947 (ttpm) REVERT: J 50 TYR cc_start: 0.8216 (p90) cc_final: 0.7906 (p90) REVERT: M 12 THR cc_start: 0.8325 (t) cc_final: 0.8033 (p) REVERT: M 43 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: L 3 GLN cc_start: 0.7551 (mp10) cc_final: 0.7283 (mp10) REVERT: L 79 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6472 (mp10) REVERT: L 85 THR cc_start: 0.7340 (m) cc_final: 0.6958 (p) REVERT: O 95 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7915 (t0) REVERT: P 106 ASP cc_start: 0.8600 (m-30) cc_final: 0.8027 (t0) REVERT: Q 53 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7447 (mttm) REVERT: R 59 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: S 83 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6351 (pm20) outliers start: 124 outliers final: 88 residues processed: 483 average time/residue: 0.1790 time to fit residues: 132.0115 Evaluate side-chains 489 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 392 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 250 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 211 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN J 58 ASN M 3 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112862 restraints weight = 33584.783| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.54 r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26347 Z= 0.177 Angle : 0.734 22.374 36035 Z= 0.331 Chirality : 0.050 0.869 4273 Planarity : 0.004 0.059 4380 Dihedral : 10.254 105.647 5665 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.77 % Allowed : 22.36 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 2986 helix: 1.25 (0.28), residues: 416 sheet: -0.40 (0.17), residues: 935 loop : -0.45 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.022 0.001 TYR R 33 PHE 0.018 0.002 PHE H 64 TRP 0.018 0.001 TRP P 50 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00411 (26185) covalent geometry : angle 0.65669 (35595) SS BOND : bond 0.00944 ( 46) SS BOND : angle 2.41544 ( 92) hydrogen bonds : bond 0.03679 ( 844) hydrogen bonds : angle 5.21725 ( 2316) link_ALPHA1-2 : bond 0.00340 ( 5) link_ALPHA1-2 : angle 1.82056 ( 15) link_ALPHA1-3 : bond 0.01033 ( 8) link_ALPHA1-3 : angle 1.64579 ( 24) link_ALPHA1-6 : bond 0.01524 ( 9) link_ALPHA1-6 : angle 2.39321 ( 27) link_BETA1-4 : bond 0.00733 ( 40) link_BETA1-4 : angle 2.73898 ( 120) link_NAG-ASN : bond 0.00575 ( 54) link_NAG-ASN : angle 3.82969 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 392 time to evaluate : 0.604 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: A 46 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7456 (pttp) REVERT: A 117 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8063 (ttpt) REVERT: A 246 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7436 (tp40) REVERT: A 500 ARG cc_start: 0.7991 (ptp-110) cc_final: 0.7609 (mtm110) REVERT: F 542 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7584 (mtm-85) REVERT: D 535 MET cc_start: 0.8136 (mpp) cc_final: 0.7907 (mpp) REVERT: B 543 ASN cc_start: 0.8544 (m-40) cc_final: 0.8190 (m110) REVERT: E 110 SER cc_start: 0.8787 (t) cc_final: 0.8324 (m) REVERT: E 490 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8556 (ttmt) REVERT: C 66 HIS cc_start: 0.5240 (OUTLIER) cc_final: 0.4983 (t-90) REVERT: C 92 GLU cc_start: 0.7844 (tt0) cc_final: 0.7372 (tm-30) REVERT: C 103 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: H 13 LYS cc_start: 0.8340 (mmtp) cc_final: 0.7520 (mmtt) REVERT: H 30 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7922 (mtt180) REVERT: I 36 TYR cc_start: 0.8419 (m-80) cc_final: 0.8184 (m-80) REVERT: M 12 THR cc_start: 0.8393 (t) cc_final: 0.8080 (p) REVERT: M 43 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: L 79 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: L 85 THR cc_start: 0.7434 (m) cc_final: 0.7074 (p) REVERT: O 95 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7970 (t0) REVERT: P 106 ASP cc_start: 0.8596 (m-30) cc_final: 0.8010 (t0) REVERT: Q 53 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7477 (mttm) REVERT: R 59 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: S 25 GLU cc_start: 0.7891 (pm20) cc_final: 0.7682 (pm20) REVERT: S 83 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6393 (pm20) outliers start: 127 outliers final: 99 residues processed: 477 average time/residue: 0.1777 time to fit residues: 128.5937 Evaluate side-chains 491 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 384 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 159 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 207 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 244 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN H 118 GLN J 58 ASN M 3 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114372 restraints weight = 33417.155| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.67 r_work: 0.3134 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26347 Z= 0.128 Angle : 0.709 24.729 36035 Z= 0.317 Chirality : 0.047 0.638 4273 Planarity : 0.004 0.057 4380 Dihedral : 9.969 104.185 5665 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.17 % Allowed : 23.00 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2986 helix: 1.37 (0.28), residues: 416 sheet: -0.36 (0.16), residues: 982 loop : -0.40 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.023 0.001 TYR R 33 PHE 0.027 0.001 PHE H 64 TRP 0.018 0.001 TRP H 50 HIS 0.004 0.001 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00283 (26185) covalent geometry : angle 0.63063 (35595) SS BOND : bond 0.00733 ( 46) SS BOND : angle 2.18368 ( 92) hydrogen bonds : bond 0.03434 ( 844) hydrogen bonds : angle 5.14443 ( 2316) link_ALPHA1-2 : bond 0.00424 ( 5) link_ALPHA1-2 : angle 1.66291 ( 15) link_ALPHA1-3 : bond 0.01096 ( 8) link_ALPHA1-3 : angle 1.59804 ( 24) link_ALPHA1-6 : bond 0.01498 ( 9) link_ALPHA1-6 : angle 2.31214 ( 27) link_BETA1-4 : bond 0.00753 ( 40) link_BETA1-4 : angle 2.61806 ( 120) link_NAG-ASN : bond 0.00716 ( 54) link_NAG-ASN : angle 3.89815 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 395 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7466 (pttp) REVERT: A 117 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7993 (ttpt) REVERT: A 246 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7404 (tp40) REVERT: A 500 ARG cc_start: 0.7999 (ptp-110) cc_final: 0.7621 (mtm110) REVERT: F 542 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7576 (mtm-85) REVERT: D 535 MET cc_start: 0.8150 (mpp) cc_final: 0.7911 (mpp) REVERT: B 543 ASN cc_start: 0.8507 (m-40) cc_final: 0.8169 (m110) REVERT: E 110 SER cc_start: 0.8757 (t) cc_final: 0.8304 (m) REVERT: E 490 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8564 (ttmt) REVERT: C 66 HIS cc_start: 0.5243 (OUTLIER) cc_final: 0.4952 (t-90) REVERT: C 92 GLU cc_start: 0.7870 (tt0) cc_final: 0.7400 (tm-30) REVERT: C 99 ASN cc_start: 0.8632 (t0) cc_final: 0.8253 (t0) REVERT: C 103 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: H 13 LYS cc_start: 0.8351 (mmtp) cc_final: 0.7530 (mmtt) REVERT: H 30 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7890 (mtt180) REVERT: H 109 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8855 (p0) REVERT: I 36 TYR cc_start: 0.8360 (m-80) cc_final: 0.8138 (m-80) REVERT: M 12 THR cc_start: 0.8339 (t) cc_final: 0.8041 (p) REVERT: M 43 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: L 3 GLN cc_start: 0.7594 (mp10) cc_final: 0.7363 (mp10) REVERT: L 79 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: L 85 THR cc_start: 0.7486 (m) cc_final: 0.7067 (p) REVERT: O 95 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7895 (t0) REVERT: P 106 ASP cc_start: 0.8558 (m-30) cc_final: 0.8004 (t0) REVERT: Q 53 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7512 (mttm) REVERT: Q 61 ARG cc_start: 0.7324 (ptt-90) cc_final: 0.7026 (ptt-90) REVERT: R 59 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: S 83 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6323 (pm20) outliers start: 111 outliers final: 88 residues processed: 469 average time/residue: 0.1915 time to fit residues: 136.1186 Evaluate side-chains 482 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 385 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 266 optimal weight: 0.0060 chunk 198 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN H 118 GLN J 58 ASN M 3 GLN L 72 ASN S 37 GLN ** S 42 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.151570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114265 restraints weight = 33654.552| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.65 r_work: 0.3150 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26347 Z= 0.137 Angle : 0.710 24.205 36035 Z= 0.318 Chirality : 0.047 0.645 4273 Planarity : 0.004 0.058 4380 Dihedral : 9.807 103.539 5665 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.20 % Allowed : 22.96 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2986 helix: 1.49 (0.28), residues: 407 sheet: -0.32 (0.16), residues: 982 loop : -0.41 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.023 0.001 TYR R 33 PHE 0.032 0.001 PHE H 64 TRP 0.018 0.001 TRP P 50 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00310 (26185) covalent geometry : angle 0.63030 (35595) SS BOND : bond 0.00740 ( 46) SS BOND : angle 2.14997 ( 92) hydrogen bonds : bond 0.03435 ( 844) hydrogen bonds : angle 5.10344 ( 2316) link_ALPHA1-2 : bond 0.00391 ( 5) link_ALPHA1-2 : angle 1.68320 ( 15) link_ALPHA1-3 : bond 0.01074 ( 8) link_ALPHA1-3 : angle 1.60513 ( 24) link_ALPHA1-6 : bond 0.01485 ( 9) link_ALPHA1-6 : angle 2.29099 ( 27) link_BETA1-4 : bond 0.00746 ( 40) link_BETA1-4 : angle 2.62285 ( 120) link_NAG-ASN : bond 0.00639 ( 54) link_NAG-ASN : angle 3.93157 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 389 time to evaluate : 1.090 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 46 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7469 (pttp) REVERT: A 117 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7945 (ttpt) REVERT: A 246 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: A 500 ARG cc_start: 0.8002 (ptp-110) cc_final: 0.7618 (mtm110) REVERT: F 542 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7571 (mtm-85) REVERT: D 535 MET cc_start: 0.8183 (mpp) cc_final: 0.7918 (mpp) REVERT: B 543 ASN cc_start: 0.8502 (m-40) cc_final: 0.8195 (m110) REVERT: E 110 SER cc_start: 0.8810 (t) cc_final: 0.8360 (m) REVERT: E 490 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8492 (ttpp) REVERT: C 66 HIS cc_start: 0.5245 (OUTLIER) cc_final: 0.4949 (t-90) REVERT: C 92 GLU cc_start: 0.7805 (tt0) cc_final: 0.7372 (tm-30) REVERT: C 103 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: H 13 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7494 (mmtt) REVERT: H 109 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8886 (p0) REVERT: I 36 TYR cc_start: 0.8380 (m-80) cc_final: 0.8149 (m-80) REVERT: M 12 THR cc_start: 0.8324 (t) cc_final: 0.8030 (p) REVERT: M 43 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: L 61 ARG cc_start: 0.6168 (mtm-85) cc_final: 0.5948 (mtm-85) REVERT: L 79 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: L 85 THR cc_start: 0.7507 (m) cc_final: 0.7079 (p) REVERT: O 22 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8334 (p) REVERT: O 95 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7866 (t0) REVERT: P 106 ASP cc_start: 0.8533 (m-30) cc_final: 0.7978 (t0) REVERT: Q 53 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7529 (mttm) REVERT: Q 61 ARG cc_start: 0.7359 (ptt-90) cc_final: 0.7071 (ptt-90) REVERT: R 59 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: S 83 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6268 (pm20) outliers start: 112 outliers final: 89 residues processed: 464 average time/residue: 0.2022 time to fit residues: 142.5391 Evaluate side-chains 483 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 384 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN H 118 GLN J 58 ASN M 3 GLN L 72 ASN S 37 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113655 restraints weight = 33787.678| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.56 r_work: 0.3122 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26347 Z= 0.169 Angle : 0.733 23.836 36035 Z= 0.331 Chirality : 0.048 0.681 4273 Planarity : 0.004 0.058 4380 Dihedral : 9.779 104.121 5665 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.09 % Allowed : 23.38 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2986 helix: 1.32 (0.28), residues: 413 sheet: -0.30 (0.17), residues: 923 loop : -0.44 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.021 0.001 TYR R 33 PHE 0.014 0.001 PHE L 87 TRP 0.017 0.001 TRP P 50 HIS 0.003 0.001 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00392 (26185) covalent geometry : angle 0.65098 (35595) SS BOND : bond 0.00802 ( 46) SS BOND : angle 2.18769 ( 92) hydrogen bonds : bond 0.03583 ( 844) hydrogen bonds : angle 5.14868 ( 2316) link_ALPHA1-2 : bond 0.00334 ( 5) link_ALPHA1-2 : angle 1.78803 ( 15) link_ALPHA1-3 : bond 0.01022 ( 8) link_ALPHA1-3 : angle 1.62933 ( 24) link_ALPHA1-6 : bond 0.01457 ( 9) link_ALPHA1-6 : angle 2.30558 ( 27) link_BETA1-4 : bond 0.00751 ( 40) link_BETA1-4 : angle 2.67428 ( 120) link_NAG-ASN : bond 0.00563 ( 54) link_NAG-ASN : angle 4.11031 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 390 time to evaluate : 0.953 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 46 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7476 (pttp) REVERT: A 117 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8005 (ttpt) REVERT: A 246 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7434 (tp40) REVERT: A 500 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7627 (mtm110) REVERT: D 535 MET cc_start: 0.8190 (mpp) cc_final: 0.7923 (mpp) REVERT: B 535 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8373 (mpp) REVERT: B 543 ASN cc_start: 0.8525 (m-40) cc_final: 0.8189 (m110) REVERT: E 110 SER cc_start: 0.8805 (t) cc_final: 0.8340 (m) REVERT: E 161 MET cc_start: 0.8987 (tpp) cc_final: 0.7941 (tpp) REVERT: E 490 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8514 (ttpp) REVERT: C 66 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.5001 (t-90) REVERT: C 92 GLU cc_start: 0.7800 (tt0) cc_final: 0.7365 (tm-30) REVERT: C 103 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: H 109 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8863 (p0) REVERT: I 36 TYR cc_start: 0.8440 (m-80) cc_final: 0.8201 (m-80) REVERT: K 37 GLN cc_start: 0.7028 (tt0) cc_final: 0.6737 (tp-100) REVERT: M 12 THR cc_start: 0.8372 (t) cc_final: 0.8068 (p) REVERT: M 43 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: L 79 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: L 85 THR cc_start: 0.7537 (m) cc_final: 0.7117 (p) REVERT: O 95 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7925 (t0) REVERT: P 106 ASP cc_start: 0.8566 (m-30) cc_final: 0.7973 (t0) REVERT: Q 53 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7508 (mttm) REVERT: Q 61 ARG cc_start: 0.7411 (ptt-90) cc_final: 0.7154 (ptt-90) REVERT: Q 65 ARG cc_start: 0.6984 (ptm-80) cc_final: 0.6428 (ptm-80) REVERT: R 59 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: S 83 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6302 (pm20) outliers start: 109 outliers final: 93 residues processed: 462 average time/residue: 0.1985 time to fit residues: 139.2608 Evaluate side-chains 487 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 384 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 41 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 282 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN J 58 ASN L 72 ASN S 37 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114401 restraints weight = 33662.055| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.68 r_work: 0.3146 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26347 Z= 0.135 Angle : 0.711 23.114 36035 Z= 0.319 Chirality : 0.047 0.641 4273 Planarity : 0.004 0.057 4380 Dihedral : 9.588 103.793 5665 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.90 % Allowed : 23.45 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2986 helix: 1.39 (0.28), residues: 414 sheet: -0.23 (0.17), residues: 958 loop : -0.40 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.015 0.001 TYR I 71 PHE 0.012 0.001 PHE Q 87 TRP 0.018 0.001 TRP H 50 HIS 0.004 0.001 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00306 (26185) covalent geometry : angle 0.63132 (35595) SS BOND : bond 0.00731 ( 46) SS BOND : angle 2.05473 ( 92) hydrogen bonds : bond 0.03444 ( 844) hydrogen bonds : angle 5.10241 ( 2316) link_ALPHA1-2 : bond 0.00404 ( 5) link_ALPHA1-2 : angle 1.68409 ( 15) link_ALPHA1-3 : bond 0.01064 ( 8) link_ALPHA1-3 : angle 1.58426 ( 24) link_ALPHA1-6 : bond 0.01427 ( 9) link_ALPHA1-6 : angle 2.27672 ( 27) link_BETA1-4 : bond 0.00760 ( 40) link_BETA1-4 : angle 2.60429 ( 120) link_NAG-ASN : bond 0.00564 ( 54) link_NAG-ASN : angle 3.98167 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 390 time to evaluate : 0.941 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: A 46 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7496 (pttp) REVERT: A 117 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7986 (ttpt) REVERT: A 246 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7418 (tp40) REVERT: A 500 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7619 (mtm110) REVERT: F 542 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7565 (mtm-85) REVERT: D 535 MET cc_start: 0.8179 (mpp) cc_final: 0.7908 (mpp) REVERT: B 535 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: B 543 ASN cc_start: 0.8497 (m-40) cc_final: 0.8162 (m110) REVERT: E 110 SER cc_start: 0.8803 (t) cc_final: 0.8358 (m) REVERT: E 490 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8355 (ttpp) REVERT: C 66 HIS cc_start: 0.5259 (OUTLIER) cc_final: 0.4984 (t-90) REVERT: C 92 GLU cc_start: 0.7751 (tt0) cc_final: 0.7371 (tm-30) REVERT: C 103 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: H 109 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8851 (p0) REVERT: I 36 TYR cc_start: 0.8390 (m-80) cc_final: 0.8188 (m-80) REVERT: M 12 THR cc_start: 0.8360 (t) cc_final: 0.8067 (p) REVERT: M 43 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: L 4 MET cc_start: 0.7082 (mmt) cc_final: 0.6748 (mmt) REVERT: L 79 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: L 85 THR cc_start: 0.7546 (m) cc_final: 0.7124 (p) REVERT: O 95 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7891 (t0) REVERT: P 106 ASP cc_start: 0.8550 (m-30) cc_final: 0.7948 (t0) REVERT: P 109 ASP cc_start: 0.8956 (p0) cc_final: 0.8750 (p0) REVERT: Q 50 ASP cc_start: 0.8431 (t0) cc_final: 0.8052 (t0) REVERT: Q 61 ARG cc_start: 0.7445 (ptt-90) cc_final: 0.7202 (ptt-90) REVERT: Q 65 ARG cc_start: 0.6959 (ptm-80) cc_final: 0.6441 (ptm-80) REVERT: R 27 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7737 (p) REVERT: R 59 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: S 83 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6263 (pm20) outliers start: 104 outliers final: 92 residues processed: 457 average time/residue: 0.1966 time to fit residues: 136.3701 Evaluate side-chains 487 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 384 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 88 CYS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 ILE Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 59 TYR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 230 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN C 411 ASN H 118 GLN J 58 ASN M 3 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112481 restraints weight = 33544.413| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.67 r_work: 0.3119 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26347 Z= 0.174 Angle : 0.736 23.030 36035 Z= 0.332 Chirality : 0.048 0.688 4273 Planarity : 0.004 0.059 4380 Dihedral : 9.573 104.737 5665 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.94 % Allowed : 23.71 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2986 helix: 1.24 (0.28), residues: 419 sheet: -0.31 (0.17), residues: 929 loop : -0.41 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.020 0.001 TYR R 33 PHE 0.014 0.002 PHE L 87 TRP 0.028 0.001 TRP J 47 HIS 0.004 0.001 HIS R 97 Details of bonding type rmsd covalent geometry : bond 0.00406 (26185) covalent geometry : angle 0.65571 (35595) SS BOND : bond 0.00796 ( 46) SS BOND : angle 2.15139 ( 92) hydrogen bonds : bond 0.03617 ( 844) hydrogen bonds : angle 5.14513 ( 2316) link_ALPHA1-2 : bond 0.00318 ( 5) link_ALPHA1-2 : angle 1.81812 ( 15) link_ALPHA1-3 : bond 0.01001 ( 8) link_ALPHA1-3 : angle 1.59238 ( 24) link_ALPHA1-6 : bond 0.01317 ( 9) link_ALPHA1-6 : angle 2.30069 ( 27) link_BETA1-4 : bond 0.00738 ( 40) link_BETA1-4 : angle 2.69348 ( 120) link_NAG-ASN : bond 0.00596 ( 54) link_NAG-ASN : angle 4.05066 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7599.33 seconds wall clock time: 130 minutes 49.33 seconds (7849.33 seconds total)