Starting phenix.real_space_refine on Thu Mar 5 10:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.map" model { file = "/net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opo_20151/03_2026/6opo_20151.cif" } resolution = 3.5 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= -0.002 sd= 0.090 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 114 5.16 5 C 13422 2.51 5 N 3588 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21441 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "D" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "m" 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: "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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.55, per 1000 atoms: 0.21 Number of scatterers: 21441 At special positions: 0 Unit cell: (155.89, 157.2, 144.1, 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 114 16.00 O 4317 8.00 N 3588 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.11 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=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.18 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.11 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.18 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.11 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.04 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS M 605 " distance=2.18 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 617 " - " ASN A 339 " " NAG A 624 " - " ASN A 397 " " NAG A 628 " - " ASN A 448 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG D 601 " - " ASN D 88 " " NAG D 617 " - " ASN D 339 " " NAG D 624 " - " ASN D 397 " " NAG D 628 " - " ASN D 448 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 616 " " NAG J 601 " - " ASN J 88 " " NAG J 617 " - " ASN J 339 " " NAG J 624 " - " ASN J 397 " " NAG J 628 " - " ASN J 448 " " NAG M 702 " - " ASN M 611 " " NAG M 703 " - " ASN M 616 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 362 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN D 234 " " NAG a 1 " - " ASN D 241 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 276 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 332 " " NAG f 1 " - " ASN D 362 " " NAG g 1 " - " ASN D 386 " " NAG h 1 " - " ASN D 392 " " NAG i 1 " - " ASN D 413 " " NAG j 1 " - " ASN J 234 " " NAG k 1 " - " ASN J 241 " " NAG l 1 " - " ASN J 262 " " NAG m 1 " - " ASN J 276 " " NAG n 1 " - " ASN J 295 " " NAG o 1 " - " ASN J 332 " " NAG p 1 " - " ASN J 362 " " NAG q 1 " - " ASN J 386 " " NAG r 1 " - " ASN J 392 " " NAG s 1 " - " ASN J 413 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 964.3 milliseconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Processing helix chain 'B' and resid 565 through 593 removed outlier: 4.216A pdb=" N THR B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 335 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 547 Processing helix chain 'F' and resid 565 through 593 removed outlier: 4.217A pdb=" N THR F 569 " --> pdb=" O MET F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'J' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN J 98 " --> pdb=" O MET J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 114 Processing helix chain 'J' and resid 335 through 353 Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 391 Processing helix chain 'J' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN J 478 " --> pdb=" O ASN J 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'M' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE M 518 " --> pdb=" O LEU M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 547 Processing helix chain 'M' and resid 565 through 593 removed outlier: 4.217A pdb=" N THR M 569 " --> pdb=" O MET M 565 " (cutoff:3.500A) Processing helix chain 'M' and resid 594 through 597 Processing helix chain 'M' and resid 618 through 626 Processing helix chain 'M' and resid 627 through 636 Processing helix chain 'M' and resid 638 through 661 Processing helix chain 'N' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.321A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 26 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY C 38 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP C 28 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC2, first strand: chain 'D' and resid 197 through 202 Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 5 removed outlier: 6.322A pdb=" N LYS G 2 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU G 96 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 4 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE G 26 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY G 38 " --> pdb=" O PHE G 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD4, first strand: chain 'J' and resid 35 through 40 Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD8, first strand: chain 'J' and resid 197 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS J 296 " --> pdb=" O GLN J 442 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS J 296 " --> pdb=" O GLN J 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR J 467 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 2 through 5 removed outlier: 6.321A pdb=" N LYS N 2 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU N 96 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL N 4 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE N 26 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY N 38 " --> pdb=" O PHE N 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP N 28 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 12 through 17 Processing sheet with id=AE7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 10 through 12 897 hydrogen bonds defined for protein. 2223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3968 1.31 - 1.44: 6065 1.44 - 1.58: 11648 1.58 - 1.71: 30 1.71 - 1.84: 144 Bond restraints: 21855 Sorted by residual: bond pdb=" C1 NAG D 624 " pdb=" O5 NAG D 624 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 21850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 23756 2.03 - 4.07: 4785 4.07 - 6.10: 901 6.10 - 8.13: 168 8.13 - 10.17: 39 Bond angle restraints: 29649 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.72e+01 angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.71e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 129.88 -9.96 1.07e+00 8.73e-01 8.66e+01 angle pdb=" C PHE D 353 " pdb=" N PRO D 354 " pdb=" CA PRO D 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C PHE J 353 " pdb=" N PRO J 354 " pdb=" CA PRO J 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.92e+01 ... (remaining 29644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 13810 21.79 - 43.57: 386 43.57 - 65.36: 132 65.36 - 87.14: 54 87.14 - 108.93: 27 Dihedral angle restraints: 14409 sinusoidal: 7047 harmonic: 7362 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.67 75.67 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 14406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2811 0.118 - 0.235: 698 0.235 - 0.353: 68 0.353 - 0.470: 14 0.470 - 0.588: 6 Chirality restraints: 3597 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 BMA b 3 " pdb=" O4 NAG b 2 " pdb=" C2 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 3594 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.059 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" C7 NAG p 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.078 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.059 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" C7 NAG V 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.90e+01 pdb=" C7 NAG f 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 8865 2.89 - 3.39: 18646 3.39 - 3.90: 36958 3.90 - 4.40: 41724 4.40 - 4.90: 68164 Nonbonded interactions: 174357 Sorted by model distance: nonbonded pdb=" N ASN D 88 " pdb=" OD1 ASN D 88 " model vdw 2.392 3.120 nonbonded pdb=" N ASN J 88 " pdb=" OD1 ASN J 88 " model vdw 2.392 3.120 nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.393 3.120 nonbonded pdb=" O5 NAG b 1 " pdb=" O6 NAG b 1 " model vdw 2.425 2.432 nonbonded pdb=" O5 NAG l 1 " pdb=" O6 NAG l 1 " model vdw 2.426 2.432 ... (remaining 174352 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'Y' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.230 Find NCS groups from input model: 0.550 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.022 0.146 21984 Z= 1.173 Angle : 1.786 10.168 29997 Z= 1.137 Chirality : 0.103 0.588 3597 Planarity : 0.009 0.049 3660 Dihedral : 13.053 108.929 9546 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.79 % Favored : 97.97 % Rotamer: Outliers : 0.41 % Allowed : 0.27 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2517 helix: 0.82 (0.23), residues: 438 sheet: 1.47 (0.20), residues: 663 loop : 0.45 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.036 0.008 TYR A 486 PHE 0.044 0.007 PHE E 98 TRP 0.055 0.011 TRP D 479 HIS 0.011 0.003 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.02220 (21855) covalent geometry : angle 1.76177 (29649) SS BOND : bond 0.04666 ( 39) SS BOND : angle 3.08482 ( 78) hydrogen bonds : bond 0.16289 ( 855) hydrogen bonds : angle 7.49237 ( 2223) link_ALPHA1-2 : bond 0.03861 ( 3) link_ALPHA1-2 : angle 3.23613 ( 9) link_ALPHA1-3 : bond 0.03153 ( 3) link_ALPHA1-3 : angle 2.01406 ( 9) link_BETA1-4 : bond 0.02830 ( 36) link_BETA1-4 : angle 3.61962 ( 108) link_NAG-ASN : bond 0.02874 ( 48) link_NAG-ASN : angle 3.05076 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 642 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7584 (t0) cc_final: 0.7298 (p0) REVERT: A 113 ASP cc_start: 0.7837 (m-30) cc_final: 0.7620 (m-30) REVERT: A 210 PHE cc_start: 0.8844 (t80) cc_final: 0.8619 (t80) REVERT: A 279 ASP cc_start: 0.7218 (p0) cc_final: 0.6614 (t0) REVERT: A 377 ASN cc_start: 0.8470 (t0) cc_final: 0.7680 (t0) REVERT: L 36 TYR cc_start: 0.6951 (m-80) cc_final: 0.6735 (m-80) REVERT: C 81 THR cc_start: 0.8697 (m) cc_final: 0.8218 (p) REVERT: H 27 ASP cc_start: 0.8064 (t0) cc_final: 0.7744 (t0) REVERT: H 100 TYR cc_start: 0.7196 (t80) cc_final: 0.6636 (t80) REVERT: H 100 ASP cc_start: 0.6086 (m-30) cc_final: 0.5754 (m-30) REVERT: D 80 ASN cc_start: 0.7900 (t0) cc_final: 0.7618 (p0) REVERT: D 95 MET cc_start: 0.8588 (ptm) cc_final: 0.8274 (ptp) REVERT: D 279 ASP cc_start: 0.6918 (p0) cc_final: 0.6157 (t0) REVERT: D 475 MET cc_start: 0.8362 (mmt) cc_final: 0.8098 (mmt) REVERT: F 617 LYS cc_start: 0.8629 (mttm) cc_final: 0.8283 (mtmt) REVERT: F 634 GLU cc_start: 0.8128 (tp30) cc_final: 0.7804 (tp30) REVERT: I 12 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7771 (mtpt) REVERT: I 82 LEU cc_start: 0.7751 (tp) cc_final: 0.7534 (tp) REVERT: I 87 THR cc_start: 0.7866 (m) cc_final: 0.7635 (t) REVERT: I 100 TYR cc_start: 0.7485 (t80) cc_final: 0.6387 (t80) REVERT: I 100 ASP cc_start: 0.5980 (m-30) cc_final: 0.5466 (m-30) REVERT: I 100 ASN cc_start: 0.6613 (t0) cc_final: 0.6357 (t0) REVERT: J 279 ASP cc_start: 0.7098 (p0) cc_final: 0.6319 (t0) REVERT: M 620 ASN cc_start: 0.7993 (m-40) cc_final: 0.7721 (m-40) REVERT: N 5 LEU cc_start: 0.8486 (tt) cc_final: 0.8246 (tt) REVERT: O 12 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7669 (mtpt) REVERT: O 19 LYS cc_start: 0.7362 (tttt) cc_final: 0.7112 (mmtt) REVERT: O 27 ASP cc_start: 0.8128 (t0) cc_final: 0.7722 (t0) REVERT: O 82 LEU cc_start: 0.7798 (tp) cc_final: 0.7587 (tp) REVERT: O 100 TYR cc_start: 0.7244 (t80) cc_final: 0.6245 (t80) REVERT: O 100 ASN cc_start: 0.6568 (t0) cc_final: 0.6290 (t0) outliers start: 9 outliers final: 2 residues processed: 648 average time/residue: 0.1730 time to fit residues: 164.4336 Evaluate side-chains 342 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 340 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain J residue 88 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 422 GLN L 89 GLN B 575 GLN B 607 ASN H 102 HIS D 72 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN I 102 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 575 GLN M 607 ASN M 652 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102004 restraints weight = 35285.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106119 restraints weight = 25338.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106862 restraints weight = 16907.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107436 restraints weight = 13779.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107751 restraints weight = 13435.497| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21984 Z= 0.193 Angle : 0.794 22.080 29997 Z= 0.407 Chirality : 0.049 0.258 3597 Planarity : 0.005 0.038 3660 Dihedral : 9.009 60.205 4783 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.12 % Allowed : 8.80 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.79 (0.16), residues: 2517 helix: 1.91 (0.24), residues: 435 sheet: 1.23 (0.20), residues: 648 loop : -0.23 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 337 TYR 0.022 0.002 TYR I 32 PHE 0.023 0.003 PHE L 98 TRP 0.018 0.002 TRP M 614 HIS 0.005 0.001 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00425 (21855) covalent geometry : angle 0.73996 (29649) SS BOND : bond 0.00479 ( 39) SS BOND : angle 1.54647 ( 78) hydrogen bonds : bond 0.05920 ( 855) hydrogen bonds : angle 5.92289 ( 2223) link_ALPHA1-2 : bond 0.00023 ( 3) link_ALPHA1-2 : angle 2.11040 ( 9) link_ALPHA1-3 : bond 0.00428 ( 3) link_ALPHA1-3 : angle 2.28741 ( 9) link_BETA1-4 : bond 0.00449 ( 36) link_BETA1-4 : angle 2.14174 ( 108) link_NAG-ASN : bond 0.00413 ( 48) link_NAG-ASN : angle 3.65705 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 403 time to evaluate : 0.828 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 74 CYS cc_start: 0.5372 (m) cc_final: 0.4931 (m) REVERT: A 80 ASN cc_start: 0.7782 (t0) cc_final: 0.7431 (p0) REVERT: A 210 PHE cc_start: 0.8787 (t80) cc_final: 0.8577 (t80) REVERT: A 305 LYS cc_start: 0.5631 (mmtp) cc_final: 0.5040 (mmpt) REVERT: A 341 THR cc_start: 0.8512 (m) cc_final: 0.8167 (p) REVERT: L 78 LEU cc_start: 0.7914 (tp) cc_final: 0.7406 (tt) REVERT: L 92 ASN cc_start: 0.8384 (t0) cc_final: 0.7938 (t0) REVERT: L 95 ARG cc_start: 0.7042 (ptp-110) cc_final: 0.6505 (mtt90) REVERT: B 518 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.5875 (t80) REVERT: B 543 LEU cc_start: 0.8526 (mp) cc_final: 0.8283 (tp) REVERT: D 80 ASN cc_start: 0.7959 (t0) cc_final: 0.7736 (p0) REVERT: D 95 MET cc_start: 0.8559 (ptm) cc_final: 0.8231 (ptp) REVERT: D 252 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8228 (mtt-85) REVERT: D 475 MET cc_start: 0.7607 (mmt) cc_final: 0.7290 (mmt) REVERT: E 49 TYR cc_start: 0.5603 (OUTLIER) cc_final: 0.5353 (t80) REVERT: E 92 ASN cc_start: 0.8477 (t0) cc_final: 0.8048 (t0) REVERT: F 518 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6120 (t80) REVERT: F 617 LYS cc_start: 0.8732 (mttm) cc_final: 0.8367 (mtmt) REVERT: F 636 ASP cc_start: 0.8495 (t0) cc_final: 0.8214 (t0) REVERT: G 12 VAL cc_start: 0.8601 (t) cc_final: 0.8248 (p) REVERT: G 94 GLN cc_start: 0.8521 (tt0) cc_final: 0.8041 (tm-30) REVERT: J 40 TYR cc_start: 0.8857 (t80) cc_final: 0.8526 (t80) REVERT: J 74 CYS cc_start: 0.5270 (m) cc_final: 0.4965 (m) REVERT: K 91 TYR cc_start: 0.4100 (m-80) cc_final: 0.3216 (m-10) REVERT: M 518 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.5937 (t80) REVERT: M 530 MET cc_start: 0.8744 (mtp) cc_final: 0.8493 (mtm) REVERT: M 620 ASN cc_start: 0.8116 (m-40) cc_final: 0.7842 (m-40) REVERT: O 19 LYS cc_start: 0.7701 (tttt) cc_final: 0.7287 (mmtt) REVERT: O 82 LEU cc_start: 0.7759 (tp) cc_final: 0.7528 (tp) REVERT: O 100 TYR cc_start: 0.6595 (t80) cc_final: 0.5699 (t80) REVERT: O 100 ASN cc_start: 0.6240 (t0) cc_final: 0.5765 (t0) outliers start: 47 outliers final: 23 residues processed: 433 average time/residue: 0.1726 time to fit residues: 110.0392 Evaluate side-chains 352 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 325 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 518 PHE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 9 optimal weight: 0.0870 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 170 optimal weight: 0.0570 chunk 189 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN B 607 ASN D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN K 100 GLN M 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105871 restraints weight = 34932.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107942 restraints weight = 28378.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109268 restraints weight = 21864.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109660 restraints weight = 17236.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109908 restraints weight = 16669.348| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21984 Z= 0.147 Angle : 0.666 11.814 29997 Z= 0.340 Chirality : 0.045 0.208 3597 Planarity : 0.004 0.043 3660 Dihedral : 7.201 52.167 4779 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.21 % Allowed : 9.92 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.58 (0.16), residues: 2517 helix: 2.02 (0.25), residues: 435 sheet: 0.92 (0.20), residues: 654 loop : -0.38 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.022 0.002 TYR E 49 PHE 0.018 0.002 PHE A 382 TRP 0.013 0.001 TRP M 571 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00325 (21855) covalent geometry : angle 0.63285 (29649) SS BOND : bond 0.00248 ( 39) SS BOND : angle 0.85886 ( 78) hydrogen bonds : bond 0.04796 ( 855) hydrogen bonds : angle 5.58638 ( 2223) link_ALPHA1-2 : bond 0.00103 ( 3) link_ALPHA1-2 : angle 1.93197 ( 9) link_ALPHA1-3 : bond 0.01245 ( 3) link_ALPHA1-3 : angle 1.38802 ( 9) link_BETA1-4 : bond 0.00448 ( 36) link_BETA1-4 : angle 1.74510 ( 108) link_NAG-ASN : bond 0.00904 ( 48) link_NAG-ASN : angle 2.63704 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 384 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7803 (ttm) REVERT: A 210 PHE cc_start: 0.8733 (t80) cc_final: 0.8528 (t80) REVERT: A 279 ASP cc_start: 0.6816 (t0) cc_final: 0.6538 (t0) REVERT: A 341 THR cc_start: 0.8520 (m) cc_final: 0.8290 (p) REVERT: A 499 THR cc_start: 0.8847 (m) cc_final: 0.8632 (m) REVERT: L 78 LEU cc_start: 0.8152 (tp) cc_final: 0.7880 (tt) REVERT: L 92 ASN cc_start: 0.8091 (t0) cc_final: 0.7593 (t0) REVERT: L 95 ARG cc_start: 0.6922 (ptp-110) cc_final: 0.6598 (mtt90) REVERT: H 28 THR cc_start: 0.8173 (p) cc_final: 0.7458 (p) REVERT: H 89 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7365 (m) REVERT: D 95 MET cc_start: 0.8124 (ptm) cc_final: 0.7831 (ptp) REVERT: D 104 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7804 (ttm) REVERT: D 475 MET cc_start: 0.7652 (mmt) cc_final: 0.7433 (mmt) REVERT: E 49 TYR cc_start: 0.4785 (OUTLIER) cc_final: 0.4244 (t80) REVERT: F 519 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8096 (mt) REVERT: F 548 ILE cc_start: 0.8547 (mm) cc_final: 0.8283 (mm) REVERT: F 636 ASP cc_start: 0.8035 (t0) cc_final: 0.7764 (t0) REVERT: F 647 GLU cc_start: 0.7009 (tt0) cc_final: 0.6337 (tt0) REVERT: J 40 TYR cc_start: 0.8933 (t80) cc_final: 0.8620 (t80) REVERT: J 80 ASN cc_start: 0.7529 (p0) cc_final: 0.7317 (p0) REVERT: J 499 THR cc_start: 0.9086 (m) cc_final: 0.8870 (m) REVERT: K 89 GLN cc_start: 0.7013 (tt0) cc_final: 0.6748 (pt0) REVERT: M 620 ASN cc_start: 0.7369 (m-40) cc_final: 0.7051 (m-40) REVERT: M 655 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8255 (ttmm) REVERT: O 66 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7106 (mtp180) REVERT: O 82 LEU cc_start: 0.7716 (tp) cc_final: 0.7460 (tp) REVERT: O 100 TYR cc_start: 0.6925 (t80) cc_final: 0.6264 (t80) outliers start: 49 outliers final: 24 residues processed: 415 average time/residue: 0.1675 time to fit residues: 103.9035 Evaluate side-chains 343 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 314 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 111 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN D 66 HIS D 374 HIS E 79 GLN E 90 GLN F 652 GLN J 66 HIS J 422 GLN K 100 GLN M 540 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099857 restraints weight = 35329.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100310 restraints weight = 30200.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100872 restraints weight = 27711.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101689 restraints weight = 23904.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102457 restraints weight = 22016.183| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21984 Z= 0.272 Angle : 0.738 7.819 29997 Z= 0.379 Chirality : 0.049 0.304 3597 Planarity : 0.005 0.053 3660 Dihedral : 6.951 55.678 4779 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 10.96 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.04 (0.16), residues: 2517 helix: 1.87 (0.25), residues: 435 sheet: 0.47 (0.20), residues: 660 loop : -0.78 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 83 TYR 0.021 0.002 TYR E 49 PHE 0.019 0.003 PHE D 53 TRP 0.018 0.002 TRP A 45 HIS 0.010 0.002 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00647 (21855) covalent geometry : angle 0.71257 (29649) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.11182 ( 78) hydrogen bonds : bond 0.05200 ( 855) hydrogen bonds : angle 5.59815 ( 2223) link_ALPHA1-2 : bond 0.00391 ( 3) link_ALPHA1-2 : angle 2.24463 ( 9) link_ALPHA1-3 : bond 0.01139 ( 3) link_ALPHA1-3 : angle 1.52885 ( 9) link_BETA1-4 : bond 0.00344 ( 36) link_BETA1-4 : angle 1.64175 ( 108) link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 2.38089 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 353 time to evaluate : 0.768 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 80 ASN cc_start: 0.7523 (p0) cc_final: 0.7294 (p0) REVERT: A 104 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7781 (ttm) REVERT: A 210 PHE cc_start: 0.8860 (t80) cc_final: 0.8647 (t80) REVERT: A 462 GLN cc_start: 0.6812 (mm110) cc_final: 0.6335 (mm110) REVERT: L 78 LEU cc_start: 0.8300 (tp) cc_final: 0.8083 (tt) REVERT: H 17 SER cc_start: 0.6775 (p) cc_final: 0.6375 (m) REVERT: H 89 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7035 (p) REVERT: D 104 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7630 (ttm) REVERT: D 404 TYR cc_start: 0.7612 (m-80) cc_final: 0.7391 (m-80) REVERT: D 434 MET cc_start: 0.7497 (ttt) cc_final: 0.7013 (ttt) REVERT: E 24 ARG cc_start: 0.6953 (ttm110) cc_final: 0.6680 (ttm110) REVERT: E 49 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.4564 (t80) REVERT: I 12 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7308 (mptt) REVERT: I 100 TYR cc_start: 0.7510 (t80) cc_final: 0.6312 (t80) REVERT: J 80 ASN cc_start: 0.7766 (p0) cc_final: 0.7449 (p0) REVERT: M 620 ASN cc_start: 0.7354 (m-40) cc_final: 0.7067 (m-40) REVERT: M 655 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8220 (ttmm) REVERT: O 1 GLN cc_start: 0.7320 (mp10) cc_final: 0.7005 (mp10) REVERT: O 100 TYR cc_start: 0.7356 (t80) cc_final: 0.6844 (t80) outliers start: 72 outliers final: 46 residues processed: 401 average time/residue: 0.1660 time to fit residues: 98.9594 Evaluate side-chains 355 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 179 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102899 restraints weight = 34959.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104053 restraints weight = 29251.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104988 restraints weight = 25797.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105591 restraints weight = 21121.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106012 restraints weight = 19815.834| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21984 Z= 0.143 Angle : 0.643 10.512 29997 Z= 0.328 Chirality : 0.045 0.314 3597 Planarity : 0.004 0.049 3660 Dihedral : 6.558 59.870 4779 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 13.13 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.10 (0.17), residues: 2517 helix: 2.01 (0.26), residues: 435 sheet: 0.52 (0.20), residues: 660 loop : -0.79 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 440 TYR 0.019 0.002 TYR L 91 PHE 0.024 0.002 PHE O 29 TRP 0.025 0.001 TRP K 35 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00330 (21855) covalent geometry : angle 0.61229 (29649) SS BOND : bond 0.00233 ( 39) SS BOND : angle 1.79390 ( 78) hydrogen bonds : bond 0.04383 ( 855) hydrogen bonds : angle 5.37344 ( 2223) link_ALPHA1-2 : bond 0.00112 ( 3) link_ALPHA1-2 : angle 2.08221 ( 9) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.01164 ( 9) link_BETA1-4 : bond 0.00338 ( 36) link_BETA1-4 : angle 1.33961 ( 108) link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 2.35189 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 0.724 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 80 ASN cc_start: 0.7627 (p0) cc_final: 0.7354 (p0) REVERT: A 104 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: A 210 PHE cc_start: 0.8635 (t80) cc_final: 0.8397 (t80) REVERT: A 462 GLN cc_start: 0.6901 (mm110) cc_final: 0.6378 (mm110) REVERT: A 475 MET cc_start: 0.7352 (mmt) cc_final: 0.7081 (mmt) REVERT: L 92 ASN cc_start: 0.8319 (t0) cc_final: 0.8082 (t0) REVERT: H 66 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6921 (mtp180) REVERT: H 89 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7422 (m) REVERT: D 104 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: D 404 TYR cc_start: 0.7746 (m-80) cc_final: 0.7532 (m-80) REVERT: D 440 ARG cc_start: 0.4997 (tpm170) cc_final: 0.4544 (tpm170) REVERT: E 24 ARG cc_start: 0.6918 (ttm110) cc_final: 0.6716 (ttm110) REVERT: F 603 ILE cc_start: 0.8638 (mt) cc_final: 0.8411 (mt) REVERT: F 626 MET cc_start: 0.7945 (mtp) cc_final: 0.7712 (mtm) REVERT: I 10 GLU cc_start: 0.5867 (tt0) cc_final: 0.5396 (tt0) REVERT: I 28 THR cc_start: 0.8146 (p) cc_final: 0.7758 (p) REVERT: I 87 THR cc_start: 0.7582 (m) cc_final: 0.7358 (t) REVERT: J 80 ASN cc_start: 0.7708 (p0) cc_final: 0.7372 (p0) REVERT: K 24 ARG cc_start: 0.6549 (ttm110) cc_final: 0.6019 (ttm-80) REVERT: M 620 ASN cc_start: 0.7196 (m-40) cc_final: 0.6912 (m-40) REVERT: M 655 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8192 (ttmm) REVERT: O 1 GLN cc_start: 0.7131 (mp10) cc_final: 0.6683 (mp10) REVERT: O 12 LYS cc_start: 0.7932 (mmpt) cc_final: 0.7533 (mmpt) REVERT: O 100 TYR cc_start: 0.7306 (t80) cc_final: 0.6853 (t80) outliers start: 43 outliers final: 25 residues processed: 387 average time/residue: 0.1669 time to fit residues: 96.3156 Evaluate side-chains 336 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 84 optimal weight: 0.5980 chunk 220 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN I 1 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103238 restraints weight = 35052.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104405 restraints weight = 28386.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105321 restraints weight = 24902.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106025 restraints weight = 20568.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106295 restraints weight = 18898.146| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21984 Z= 0.135 Angle : 0.629 10.587 29997 Z= 0.323 Chirality : 0.045 0.238 3597 Planarity : 0.004 0.046 3660 Dihedral : 6.199 59.929 4779 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 13.67 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.17 (0.17), residues: 2517 helix: 2.13 (0.26), residues: 435 sheet: 0.54 (0.20), residues: 660 loop : -0.75 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.021 0.001 TYR L 91 PHE 0.046 0.002 PHE H 29 TRP 0.031 0.001 TRP L 35 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00308 (21855) covalent geometry : angle 0.60086 (29649) SS BOND : bond 0.00321 ( 39) SS BOND : angle 2.17789 ( 78) hydrogen bonds : bond 0.04140 ( 855) hydrogen bonds : angle 5.32823 ( 2223) link_ALPHA1-2 : bond 0.00199 ( 3) link_ALPHA1-2 : angle 2.18437 ( 9) link_ALPHA1-3 : bond 0.01065 ( 3) link_ALPHA1-3 : angle 0.96868 ( 9) link_BETA1-4 : bond 0.00355 ( 36) link_BETA1-4 : angle 1.27505 ( 108) link_NAG-ASN : bond 0.00181 ( 48) link_NAG-ASN : angle 1.96274 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 342 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7654 (p0) cc_final: 0.7366 (p0) REVERT: A 104 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: A 462 GLN cc_start: 0.7082 (mm110) cc_final: 0.6401 (mm110) REVERT: A 475 MET cc_start: 0.7379 (mmt) cc_final: 0.7085 (mmt) REVERT: B 542 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7871 (ttp-110) REVERT: H 66 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6813 (mtp180) REVERT: H 89 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7403 (m) REVERT: D 104 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7705 (ttm) REVERT: E 79 GLN cc_start: 0.7873 (mp10) cc_final: 0.7241 (mp10) REVERT: F 603 ILE cc_start: 0.8656 (mt) cc_final: 0.8444 (mt) REVERT: F 626 MET cc_start: 0.7961 (mtp) cc_final: 0.7733 (mtm) REVERT: G 94 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7415 (tt0) REVERT: I 12 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7842 (mmmt) REVERT: J 80 ASN cc_start: 0.7760 (p0) cc_final: 0.7420 (p0) REVERT: M 620 ASN cc_start: 0.7589 (m-40) cc_final: 0.7276 (m110) REVERT: M 655 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8194 (ttmm) REVERT: O 1 GLN cc_start: 0.7110 (mp10) cc_final: 0.6641 (mp10) REVERT: O 12 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7618 (mmpt) REVERT: O 100 TYR cc_start: 0.7376 (t80) cc_final: 0.6932 (t80) outliers start: 50 outliers final: 31 residues processed: 378 average time/residue: 0.1667 time to fit residues: 94.6466 Evaluate side-chains 343 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 103 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN J 72 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104440 restraints weight = 34951.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104976 restraints weight = 31456.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105944 restraints weight = 30071.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106431 restraints weight = 23636.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106622 restraints weight = 22701.808| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21984 Z= 0.148 Angle : 0.651 10.692 29997 Z= 0.331 Chirality : 0.046 0.331 3597 Planarity : 0.004 0.048 3660 Dihedral : 6.080 59.857 4779 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 14.39 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.11 (0.17), residues: 2517 helix: 1.94 (0.26), residues: 453 sheet: 0.68 (0.20), residues: 642 loop : -0.86 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 24 TYR 0.020 0.002 TYR O 79 PHE 0.036 0.002 PHE I 29 TRP 0.022 0.001 TRP L 35 HIS 0.007 0.001 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00345 (21855) covalent geometry : angle 0.61559 (29649) SS BOND : bond 0.00284 ( 39) SS BOND : angle 1.96355 ( 78) hydrogen bonds : bond 0.04118 ( 855) hydrogen bonds : angle 5.27428 ( 2223) link_ALPHA1-2 : bond 0.00164 ( 3) link_ALPHA1-2 : angle 2.19637 ( 9) link_ALPHA1-3 : bond 0.00975 ( 3) link_ALPHA1-3 : angle 0.94729 ( 9) link_BETA1-4 : bond 0.00348 ( 36) link_BETA1-4 : angle 1.25729 ( 108) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.59829 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 326 time to evaluate : 0.823 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 80 ASN cc_start: 0.7523 (p0) cc_final: 0.7199 (p0) REVERT: A 104 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7905 (ttm) REVERT: A 377 ASN cc_start: 0.7910 (t0) cc_final: 0.7696 (t0) REVERT: A 462 GLN cc_start: 0.6959 (mm110) cc_final: 0.6417 (mm110) REVERT: A 475 MET cc_start: 0.7381 (mmt) cc_final: 0.7108 (mmt) REVERT: L 3 GLU cc_start: 0.7414 (pp20) cc_final: 0.7140 (pm20) REVERT: H 10 GLU cc_start: 0.6052 (tp30) cc_final: 0.5792 (tt0) REVERT: H 89 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7498 (m) REVERT: D 104 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: G 94 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7434 (tt0) REVERT: I 12 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7656 (mmpt) REVERT: J 80 ASN cc_start: 0.7713 (p0) cc_final: 0.7345 (p0) REVERT: K 78 LEU cc_start: 0.7954 (tp) cc_final: 0.7464 (tt) REVERT: M 620 ASN cc_start: 0.7324 (m-40) cc_final: 0.7063 (m110) REVERT: M 655 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8189 (ttmm) REVERT: O 1 GLN cc_start: 0.7148 (mp10) cc_final: 0.6768 (mp10) REVERT: O 100 TYR cc_start: 0.7377 (t80) cc_final: 0.6955 (t80) outliers start: 48 outliers final: 37 residues processed: 355 average time/residue: 0.1718 time to fit residues: 90.3232 Evaluate side-chains 345 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 30 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 chunk 168 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN J 72 HIS K 79 GLN K 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103787 restraints weight = 34860.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105612 restraints weight = 28657.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106957 restraints weight = 22165.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107310 restraints weight = 18414.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107555 restraints weight = 17613.701| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21984 Z= 0.123 Angle : 0.627 9.233 29997 Z= 0.319 Chirality : 0.045 0.278 3597 Planarity : 0.004 0.045 3660 Dihedral : 5.919 57.065 4779 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.12 % Allowed : 15.11 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.14 (0.17), residues: 2517 helix: 1.90 (0.26), residues: 459 sheet: 0.62 (0.20), residues: 660 loop : -0.81 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.016 0.001 TYR E 49 PHE 0.033 0.002 PHE H 29 TRP 0.013 0.001 TRP L 35 HIS 0.019 0.001 HIS J 72 Details of bonding type rmsd covalent geometry : bond 0.00278 (21855) covalent geometry : angle 0.59864 (29649) SS BOND : bond 0.00256 ( 39) SS BOND : angle 1.79643 ( 78) hydrogen bonds : bond 0.03890 ( 855) hydrogen bonds : angle 5.22905 ( 2223) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 2.16096 ( 9) link_ALPHA1-3 : bond 0.00939 ( 3) link_ALPHA1-3 : angle 0.86881 ( 9) link_BETA1-4 : bond 0.00382 ( 36) link_BETA1-4 : angle 1.21140 ( 108) link_NAG-ASN : bond 0.00237 ( 48) link_NAG-ASN : angle 2.20244 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 327 time to evaluate : 0.892 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 80 ASN cc_start: 0.7610 (p0) cc_final: 0.7274 (p0) REVERT: A 104 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: A 475 MET cc_start: 0.7336 (mmt) cc_final: 0.6990 (mmt) REVERT: L 89 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: B 659 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7822 (tm-30) REVERT: H 10 GLU cc_start: 0.6188 (tp30) cc_final: 0.5852 (tt0) REVERT: H 89 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7427 (m) REVERT: D 104 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7780 (ttm) REVERT: D 440 ARG cc_start: 0.4429 (tpm170) cc_final: 0.4160 (tpm170) REVERT: E 24 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6337 (ttm110) REVERT: E 30 SER cc_start: 0.8601 (m) cc_final: 0.8359 (p) REVERT: E 79 GLN cc_start: 0.7794 (mp10) cc_final: 0.7184 (mp10) REVERT: G 53 ASP cc_start: 0.8122 (p0) cc_final: 0.7843 (p0) REVERT: G 94 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7530 (tt0) REVERT: I 66 ARG cc_start: 0.6806 (ttp80) cc_final: 0.6443 (ttt180) REVERT: J 80 ASN cc_start: 0.7801 (p0) cc_final: 0.7438 (p0) REVERT: K 78 LEU cc_start: 0.7940 (tp) cc_final: 0.7527 (tt) REVERT: M 620 ASN cc_start: 0.7419 (m-40) cc_final: 0.7176 (m110) REVERT: M 655 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8230 (ttmm) REVERT: O 1 GLN cc_start: 0.7109 (mp10) cc_final: 0.6723 (mp10) REVERT: O 12 LYS cc_start: 0.7919 (mmpt) cc_final: 0.7309 (tppt) REVERT: O 82 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6248 (ptp90) REVERT: O 100 ASP cc_start: 0.8122 (t0) cc_final: 0.7843 (t0) REVERT: O 100 TYR cc_start: 0.7378 (t80) cc_final: 0.6895 (t80) outliers start: 47 outliers final: 30 residues processed: 360 average time/residue: 0.1627 time to fit residues: 88.0370 Evaluate side-chains 340 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 79 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 168 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 100 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS K 89 GLN K 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102496 restraints weight = 34945.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102923 restraints weight = 28887.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104042 restraints weight = 26892.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104458 restraints weight = 22021.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104695 restraints weight = 20628.453| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21984 Z= 0.179 Angle : 0.669 9.995 29997 Z= 0.342 Chirality : 0.046 0.262 3597 Planarity : 0.004 0.045 3660 Dihedral : 6.035 58.795 4779 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.98 % Allowed : 15.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.10 (0.17), residues: 2517 helix: 1.90 (0.26), residues: 459 sheet: 0.73 (0.21), residues: 627 loop : -0.89 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 83 TYR 0.019 0.002 TYR H 79 PHE 0.035 0.002 PHE O 29 TRP 0.022 0.001 TRP J 479 HIS 0.018 0.001 HIS J 72 Details of bonding type rmsd covalent geometry : bond 0.00425 (21855) covalent geometry : angle 0.64094 (29649) SS BOND : bond 0.00312 ( 39) SS BOND : angle 2.09134 ( 78) hydrogen bonds : bond 0.04214 ( 855) hydrogen bonds : angle 5.30665 ( 2223) link_ALPHA1-2 : bond 0.00208 ( 3) link_ALPHA1-2 : angle 2.26066 ( 9) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 0.98540 ( 9) link_BETA1-4 : bond 0.00329 ( 36) link_BETA1-4 : angle 1.26010 ( 108) link_NAG-ASN : bond 0.00184 ( 48) link_NAG-ASN : angle 2.14927 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 323 time to evaluate : 0.682 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 80 ASN cc_start: 0.7536 (p0) cc_final: 0.7193 (p0) REVERT: A 104 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7929 (ttm) REVERT: L 79 GLN cc_start: 0.7577 (mp10) cc_final: 0.7129 (mt0) REVERT: L 92 ASN cc_start: 0.8332 (t0) cc_final: 0.7909 (t0) REVERT: H 10 GLU cc_start: 0.6300 (tp30) cc_final: 0.5875 (tt0) REVERT: D 104 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: E 24 ARG cc_start: 0.6752 (ttm110) cc_final: 0.6341 (ttm110) REVERT: E 30 SER cc_start: 0.8587 (m) cc_final: 0.8387 (p) REVERT: E 79 GLN cc_start: 0.7911 (mp10) cc_final: 0.7273 (mp10) REVERT: G 94 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7475 (tt0) REVERT: I 66 ARG cc_start: 0.6667 (ttp80) cc_final: 0.6167 (ttt180) REVERT: J 80 ASN cc_start: 0.7738 (p0) cc_final: 0.7333 (p0) REVERT: J 479 TRP cc_start: 0.7935 (m-90) cc_final: 0.7690 (m-90) REVERT: K 78 LEU cc_start: 0.8074 (tp) cc_final: 0.7691 (tt) REVERT: M 620 ASN cc_start: 0.7556 (m-40) cc_final: 0.6685 (m-40) REVERT: M 655 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8199 (ttmm) REVERT: O 1 GLN cc_start: 0.7193 (mp10) cc_final: 0.6792 (mp10) REVERT: O 66 ARG cc_start: 0.6768 (mtp180) cc_final: 0.6477 (mtp180) REVERT: O 82 ARG cc_start: 0.6551 (ptp90) cc_final: 0.6253 (ptp90) REVERT: O 100 TYR cc_start: 0.7401 (t80) cc_final: 0.6921 (t80) outliers start: 44 outliers final: 34 residues processed: 351 average time/residue: 0.1717 time to fit residues: 89.5580 Evaluate side-chains 347 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 45 optimal weight: 7.9990 chunk 241 optimal weight: 0.3980 chunk 226 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 100 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103513 restraints weight = 35053.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104727 restraints weight = 28881.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105607 restraints weight = 25933.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106285 restraints weight = 20858.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106633 restraints weight = 19619.252| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21984 Z= 0.142 Angle : 0.648 9.208 29997 Z= 0.330 Chirality : 0.045 0.256 3597 Planarity : 0.004 0.068 3660 Dihedral : 5.910 57.889 4779 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 15.88 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.12 (0.17), residues: 2517 helix: 1.95 (0.26), residues: 459 sheet: 0.76 (0.21), residues: 627 loop : -0.90 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 103 TYR 0.035 0.002 TYR L 91 PHE 0.035 0.002 PHE O 29 TRP 0.031 0.001 TRP J 479 HIS 0.007 0.001 HIS O 62 Details of bonding type rmsd covalent geometry : bond 0.00332 (21855) covalent geometry : angle 0.62357 (29649) SS BOND : bond 0.00277 ( 39) SS BOND : angle 1.81019 ( 78) hydrogen bonds : bond 0.04025 ( 855) hydrogen bonds : angle 5.26755 ( 2223) link_ALPHA1-2 : bond 0.00184 ( 3) link_ALPHA1-2 : angle 2.18877 ( 9) link_ALPHA1-3 : bond 0.00917 ( 3) link_ALPHA1-3 : angle 0.93109 ( 9) link_BETA1-4 : bond 0.00345 ( 36) link_BETA1-4 : angle 1.21159 ( 108) link_NAG-ASN : bond 0.00180 ( 48) link_NAG-ASN : angle 2.02861 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 0.783 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 80 ASN cc_start: 0.7553 (p0) cc_final: 0.7210 (p0) REVERT: A 104 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7924 (ttm) REVERT: L 79 GLN cc_start: 0.7644 (mp10) cc_final: 0.7264 (mt0) REVERT: L 92 ASN cc_start: 0.8259 (t0) cc_final: 0.7782 (t0) REVERT: H 10 GLU cc_start: 0.5955 (tp30) cc_final: 0.5633 (tt0) REVERT: D 104 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7726 (ttm) REVERT: E 24 ARG cc_start: 0.6669 (ttm110) cc_final: 0.6255 (ttm110) REVERT: E 79 GLN cc_start: 0.7920 (mp10) cc_final: 0.7298 (mp10) REVERT: G 94 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7518 (tt0) REVERT: I 12 LYS cc_start: 0.8049 (mmpt) cc_final: 0.7834 (mmmt) REVERT: I 66 ARG cc_start: 0.6375 (ttp80) cc_final: 0.6154 (ttt180) REVERT: J 80 ASN cc_start: 0.7671 (p0) cc_final: 0.7417 (p0) REVERT: K 3 GLU cc_start: 0.7569 (pp20) cc_final: 0.6935 (pm20) REVERT: K 78 LEU cc_start: 0.8018 (tp) cc_final: 0.7634 (tt) REVERT: M 655 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8239 (ttmm) REVERT: O 1 GLN cc_start: 0.7183 (mp10) cc_final: 0.6775 (mp10) REVERT: O 100 TYR cc_start: 0.7391 (t80) cc_final: 0.6895 (t80) outliers start: 39 outliers final: 34 residues processed: 347 average time/residue: 0.1626 time to fit residues: 84.1152 Evaluate side-chains 345 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104139 restraints weight = 35105.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104733 restraints weight = 28569.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105978 restraints weight = 26363.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106464 restraints weight = 21264.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107038 restraints weight = 20184.410| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21984 Z= 0.135 Angle : 0.642 9.329 29997 Z= 0.330 Chirality : 0.045 0.251 3597 Planarity : 0.004 0.067 3660 Dihedral : 5.760 53.762 4779 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.67 % Allowed : 16.42 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.11 (0.17), residues: 2517 helix: 1.97 (0.26), residues: 459 sheet: 0.71 (0.21), residues: 663 loop : -0.93 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 103 TYR 0.027 0.001 TYR K 91 PHE 0.034 0.002 PHE H 29 TRP 0.064 0.001 TRP J 479 HIS 0.007 0.001 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00312 (21855) covalent geometry : angle 0.61988 (29649) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.70163 ( 78) hydrogen bonds : bond 0.03928 ( 855) hydrogen bonds : angle 5.21919 ( 2223) link_ALPHA1-2 : bond 0.00203 ( 3) link_ALPHA1-2 : angle 2.20388 ( 9) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 0.97392 ( 9) link_BETA1-4 : bond 0.00343 ( 36) link_BETA1-4 : angle 1.19549 ( 108) link_NAG-ASN : bond 0.00184 ( 48) link_NAG-ASN : angle 1.92353 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.36 seconds wall clock time: 58 minutes 38.90 seconds (3518.90 seconds total)