Starting phenix.real_space_refine on Sat Jul 4 12:08:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rso_24676/07_2026/7rso_24676.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 120 5.16 5 C 12888 2.51 5 N 3348 2.21 5 O 4212 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} 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 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 chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.77, per 1000 atoms: 0.23 Number of scatterers: 20568 At special positions: 0 Unit cell: (146.72, 150.65, 121.83, 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 120 16.00 O 4212 8.00 N 3348 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.06 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.06 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.06 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 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 F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN b 4 " - " MAN b 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA Q 3 " - " MAN Q 5 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 5 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG 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 m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 230 " " NAG A 604 " - " ASN A 325 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 405 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 188 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 462 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 230 " " NAG C 604 " - " ASN C 325 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 289 " " NAG C 610 " - " ASN C 188 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 462 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 88 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 325 " " NAG D 605 " - " ASN D 355 " " NAG D 606 " - " ASN D 392 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 405 " " NAG D 609 " - " ASN D 289 " " NAG D 610 " - " ASN D 188 " " NAG D 611 " - " ASN D 160 " " NAG D 612 " - " ASN D 462 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 625 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 339 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 413 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 339 " " NAG f 1 " - " ASN C 386 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 413 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN D 156 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 241 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 448 " " NAG q 1 " - " ASN D 339 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 130 " " NAG t 1 " - " ASN D 295 " " NAG u 1 " - " ASN D 413 " " NAG v 1 " - " ASN D 332 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 814.9 milliseconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 23.3% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.787A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.342A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.659A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'I' and resid 25 through 30 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 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 67 through 68 removed outlier: 6.209A pdb=" N ASN A 67 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.210A pdb=" N ASN C 67 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN D 67 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'D' and resid 154 through 162 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE D 468 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.564A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 6118 1.35 - 1.50: 7224 1.50 - 1.66: 7475 1.66 - 1.81: 108 1.81 - 1.97: 54 Bond restraints: 20979 Sorted by residual: bond pdb=" CB TYR G 100E" pdb=" CG TYR G 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB TYR I 100E" pdb=" CG TYR I 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.55e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.54e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 20974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 28391 7.28 - 14.56: 61 14.56 - 21.85: 0 21.85 - 29.13: 0 29.13 - 36.41: 6 Bond angle restraints: 28458 Sorted by residual: angle pdb=" C2 NAG C 609 " pdb=" N2 NAG C 609 " pdb=" C7 NAG C 609 " ideal model delta sigma weight residual 124.56 160.97 -36.41 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 609 " pdb=" N2 NAG D 609 " pdb=" C7 NAG D 609 " ideal model delta sigma weight residual 124.56 160.96 -36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG v 2 " pdb=" N2 NAG v 2 " pdb=" C7 NAG v 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C2 NAG j 2 " pdb=" N2 NAG j 2 " pdb=" C7 NAG j 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 ... (remaining 28453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 10915 17.26 - 34.53: 311 34.53 - 51.79: 102 51.79 - 69.05: 42 69.05 - 86.31: 21 Dihedral angle restraints: 11391 sinusoidal: 4635 harmonic: 6756 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 74 " pdb=" CB CYS D 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 11388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2096 0.100 - 0.200: 813 0.200 - 0.300: 358 0.300 - 0.399: 195 0.399 - 0.499: 120 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.13e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.12e+02 ... (remaining 3579 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG p 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG R 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.211 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG d 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7714 2.91 - 3.40: 18478 3.40 - 3.90: 34610 3.90 - 4.40: 39772 4.40 - 4.90: 61451 Nonbonded interactions: 162025 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 432 " model vdw 2.407 3.120 nonbonded pdb=" OE2 GLU A 290 " pdb=" NZ LYS A 337 " model vdw 2.429 3.120 nonbonded pdb=" OE2 GLU C 290 " pdb=" NZ LYS C 337 " model vdw 2.429 3.120 ... (remaining 162020 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'W' selection = chain 'a' selection = chain 'i' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'c' selection = chain 'o' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.660 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.024 0.164 21156 Z= 1.228 Angle : 1.900 36.410 28956 Z= 1.152 Chirality : 0.161 0.499 3582 Planarity : 0.009 0.133 3417 Dihedral : 10.861 86.313 6936 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2307 helix: 0.03 (0.22), residues: 444 sheet: 0.89 (0.18), residues: 738 loop : 0.67 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.047 0.009 TYR I 100E PHE 0.036 0.005 PHE G 76 TRP 0.050 0.010 TRP K 35 HIS 0.008 0.003 HIS G 35A Details of bonding type rmsd/Z covalent geometry : bond 0.02293 / 1.19 (20979) covalent geometry : angle 1.85268 / 1.15 (28458) SS BOND : bond 0.01027 / 0.65 ( 33) SS BOND : angle 3.35506 / 2.03 ( 66) hydrogen bonds : bond 0.18357 / 12.18 ( 735) hydrogen bonds : angle 7.38723 / 5.13 ( 1926) link_ALPHA1-2 : bond 0.07707 / 3.86 ( 3) link_ALPHA1-2 : angle 4.30365 / 2.24 ( 9) link_ALPHA1-3 : bond 0.08550 / 4.42 ( 6) link_ALPHA1-3 : angle 4.75559 / 2.56 ( 18) link_ALPHA1-6 : bond 0.05886 / 3.07 ( 6) link_ALPHA1-6 : angle 3.23750 / 1.73 ( 18) link_BETA1-4 : bond 0.07711 / 4.83 ( 48) link_BETA1-4 : angle 5.05283 / 3.48 ( 144) link_NAG-ASN : bond 0.08409 / 5.22 ( 81) link_NAG-ASN : angle 2.63756 / 1.83 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 899 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7636 (ptm) cc_final: 0.7141 (ptm) REVERT: A 98 ASN cc_start: 0.8542 (t0) cc_final: 0.7524 (m-40) REVERT: A 100 MET cc_start: 0.7323 (mtp) cc_final: 0.6822 (ttm) REVERT: A 110 SER cc_start: 0.9470 (m) cc_final: 0.9136 (t) REVERT: A 129 LEU cc_start: 0.9263 (mt) cc_final: 0.8768 (mp) REVERT: A 131 CYS cc_start: 0.5903 (p) cc_final: 0.5649 (p) REVERT: A 338 TRP cc_start: 0.9110 (t-100) cc_final: 0.8732 (t-100) REVERT: A 377 ASN cc_start: 0.8320 (t0) cc_final: 0.8068 (t0) REVERT: B 584 GLU cc_start: 0.8891 (tt0) cc_final: 0.8666 (tt0) REVERT: B 601 LYS cc_start: 0.8816 (mttt) cc_final: 0.8610 (mtmm) REVERT: B 634 GLU cc_start: 0.8132 (tt0) cc_final: 0.7622 (tp30) REVERT: H 9 SER cc_start: 0.8153 (m) cc_final: 0.7824 (p) REVERT: H 33 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7345 (mp0) REVERT: H 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.7908 (tt0) REVERT: H 100 TRP cc_start: 0.8294 (m-10) cc_final: 0.7922 (m-10) REVERT: H 108 LEU cc_start: 0.9201 (tp) cc_final: 0.8995 (tp) REVERT: L 78 MET cc_start: 0.8379 (mmm) cc_final: 0.8116 (mmm) REVERT: L 96 GLU cc_start: 0.8311 (pt0) cc_final: 0.7609 (pt0) REVERT: C 95 MET cc_start: 0.8138 (ptm) cc_final: 0.7348 (ptm) REVERT: C 98 ASN cc_start: 0.8340 (t0) cc_final: 0.7289 (m110) REVERT: C 100 MET cc_start: 0.7952 (mtp) cc_final: 0.7316 (ttm) REVERT: C 110 SER cc_start: 0.9462 (m) cc_final: 0.9186 (t) REVERT: C 297 THR cc_start: 0.9273 (m) cc_final: 0.9017 (p) REVERT: C 377 ASN cc_start: 0.8348 (t0) cc_final: 0.8067 (t0) REVERT: C 427 TRP cc_start: 0.8415 (m-90) cc_final: 0.8078 (m-90) REVERT: C 474 ASP cc_start: 0.7449 (t0) cc_final: 0.7199 (t0) REVERT: E 540 GLN cc_start: 0.8320 (mm110) cc_final: 0.7839 (mm-40) REVERT: E 590 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9043 (tp40) REVERT: E 592 LEU cc_start: 0.9399 (tp) cc_final: 0.9146 (mt) REVERT: E 593 LEU cc_start: 0.8957 (mt) cc_final: 0.8709 (mm) REVERT: E 601 LYS cc_start: 0.8919 (mttt) cc_final: 0.8628 (mtmm) REVERT: E 616 ASN cc_start: 0.8100 (p0) cc_final: 0.7812 (p0) REVERT: E 634 GLU cc_start: 0.7871 (tt0) cc_final: 0.7505 (tp30) REVERT: E 639 THR cc_start: 0.8550 (m) cc_final: 0.8265 (p) REVERT: D 95 MET cc_start: 0.7950 (ptm) cc_final: 0.7670 (ptm) REVERT: D 98 ASN cc_start: 0.8295 (t0) cc_final: 0.7316 (m110) REVERT: D 104 MET cc_start: 0.8444 (ttm) cc_final: 0.7832 (tpp) REVERT: D 110 SER cc_start: 0.9344 (m) cc_final: 0.9019 (t) REVERT: D 165 VAL cc_start: 0.7750 (t) cc_final: 0.7513 (t) REVERT: D 217 TYR cc_start: 0.8133 (m-80) cc_final: 0.7189 (m-80) REVERT: D 352 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8413 (mm-40) REVERT: D 371 ILE cc_start: 0.8501 (mm) cc_final: 0.8201 (mm) REVERT: D 377 ASN cc_start: 0.8574 (t0) cc_final: 0.8155 (t0) REVERT: F 540 GLN cc_start: 0.8257 (mm110) cc_final: 0.7681 (mm-40) REVERT: F 601 LYS cc_start: 0.8918 (mttt) cc_final: 0.8499 (mttm) REVERT: F 634 GLU cc_start: 0.8339 (tt0) cc_final: 0.7926 (tp30) REVERT: G 36 TRP cc_start: 0.9295 (m100) cc_final: 0.8609 (m100) REVERT: G 89 THR cc_start: 0.9350 (m) cc_final: 0.8932 (p) REVERT: G 99 THR cc_start: 0.6348 (p) cc_final: 0.6077 (p) REVERT: G 100 GLN cc_start: 0.8285 (tt0) cc_final: 0.7561 (tt0) REVERT: J 33 MET cc_start: 0.8009 (ttm) cc_final: 0.7446 (mpp) REVERT: I 33 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7311 (mp0) REVERT: I 57 ASN cc_start: 0.9065 (t0) cc_final: 0.8804 (t0) REVERT: I 89 THR cc_start: 0.9405 (m) cc_final: 0.8984 (p) REVERT: I 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.8114 (tt0) REVERT: K 96 GLU cc_start: 0.8508 (pt0) cc_final: 0.8290 (pt0) outliers start: 3 outliers final: 0 residues processed: 902 average time/residue: 0.1715 time to fit residues: 228.8694 Evaluate side-chains 455 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 57 ASN L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN E 575 GLN E 653 GLN D 99 ASN D 103 GLN J 6 GLN J 32 HIS J 42 GLN I 39 GLN I 95 GLN K 6 GLN K 32 HIS K 42 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102317 restraints weight = 42815.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105678 restraints weight = 27834.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107927 restraints weight = 21132.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109453 restraints weight = 17688.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110354 restraints weight = 15712.893| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21156 Z= 0.195 Angle : 0.888 22.241 28956 Z= 0.426 Chirality : 0.056 0.829 3582 Planarity : 0.006 0.059 3417 Dihedral : 5.201 22.621 2508 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.24 % Allowed : 3.00 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.68 (0.17), residues: 2307 helix: 1.13 (0.23), residues: 429 sheet: 0.56 (0.18), residues: 777 loop : 0.24 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 31 TYR 0.033 0.002 TYR E 643 PHE 0.035 0.002 PHE I 58 TRP 0.019 0.002 TRP F 596 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (20979) covalent geometry : angle 0.78014 / 0.40 (28458) SS BOND : bond 0.00575 / 0.38 ( 33) SS BOND : angle 1.14001 / 0.72 ( 66) hydrogen bonds : bond 0.05912 / 3.90 ( 735) hydrogen bonds : angle 6.22446 / 4.31 ( 1926) link_ALPHA1-2 : bond 0.01277 / 0.64 ( 3) link_ALPHA1-2 : angle 1.98958 / 1.02 ( 9) link_ALPHA1-3 : bond 0.01290 / 0.61 ( 6) link_ALPHA1-3 : angle 2.09556 / 1.10 ( 18) link_ALPHA1-6 : bond 0.00734 / 0.40 ( 6) link_ALPHA1-6 : angle 1.27393 / 0.62 ( 18) link_BETA1-4 : bond 0.01150 / 0.65 ( 48) link_BETA1-4 : angle 2.98319 / 2.09 ( 144) link_NAG-ASN : bond 0.00865 / 0.63 ( 81) link_NAG-ASN : angle 4.06303 / 2.49 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 631 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.7576 (m-80) cc_final: 0.6829 (m-80) REVERT: A 302 ASN cc_start: 0.8438 (m110) cc_final: 0.8136 (m-40) REVERT: A 333 ILE cc_start: 0.9243 (mt) cc_final: 0.8933 (tp) REVERT: A 414 ILE cc_start: 0.8807 (mt) cc_final: 0.8563 (mt) REVERT: B 634 GLU cc_start: 0.8417 (tt0) cc_final: 0.7949 (tp30) REVERT: B 644 ASN cc_start: 0.8066 (m110) cc_final: 0.7862 (m-40) REVERT: H 33 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6551 (mp0) REVERT: H 39 GLN cc_start: 0.8828 (tp40) cc_final: 0.8616 (tp40) REVERT: H 89 THR cc_start: 0.9135 (m) cc_final: 0.8758 (p) REVERT: H 100 GLN cc_start: 0.7849 (tt0) cc_final: 0.7385 (tt0) REVERT: H 100 TRP cc_start: 0.8037 (m-10) cc_final: 0.7805 (m-10) REVERT: H 108 LEU cc_start: 0.9266 (tp) cc_final: 0.9034 (tp) REVERT: L 5 THR cc_start: 0.7902 (m) cc_final: 0.7170 (p) REVERT: L 17 GLU cc_start: 0.7980 (pt0) cc_final: 0.7536 (pm20) REVERT: L 30 TYR cc_start: 0.6712 (m-80) cc_final: 0.5794 (m-80) REVERT: L 96 GLU cc_start: 0.8228 (pt0) cc_final: 0.7427 (pt0) REVERT: C 217 TYR cc_start: 0.7914 (m-10) cc_final: 0.7648 (m-10) REVERT: C 430 VAL cc_start: 0.8921 (t) cc_final: 0.8685 (m) REVERT: E 539 VAL cc_start: 0.9221 (t) cc_final: 0.8909 (p) REVERT: E 540 GLN cc_start: 0.8470 (mm110) cc_final: 0.7632 (mm-40) REVERT: E 601 LYS cc_start: 0.8697 (mttt) cc_final: 0.8283 (mtmm) REVERT: E 616 ASN cc_start: 0.8015 (p0) cc_final: 0.7613 (p0) REVERT: E 634 GLU cc_start: 0.8329 (tt0) cc_final: 0.7836 (tp30) REVERT: E 639 THR cc_start: 0.8958 (m) cc_final: 0.8254 (p) REVERT: E 653 GLN cc_start: 0.8483 (tm130) cc_final: 0.8142 (tm-30) REVERT: D 69 TRP cc_start: 0.6163 (p-90) cc_final: 0.5359 (p-90) REVERT: D 111 LEU cc_start: 0.8877 (tp) cc_final: 0.8358 (tp) REVERT: D 180 ASP cc_start: 0.8564 (m-30) cc_final: 0.8309 (m-30) REVERT: D 217 TYR cc_start: 0.7857 (m-80) cc_final: 0.7040 (m-80) REVERT: D 373 MET cc_start: 0.8410 (mtm) cc_final: 0.8192 (mtm) REVERT: D 430 VAL cc_start: 0.8951 (t) cc_final: 0.8744 (m) REVERT: F 540 GLN cc_start: 0.8407 (mm110) cc_final: 0.7545 (mm-40) REVERT: F 584 GLU cc_start: 0.8647 (tt0) cc_final: 0.8408 (tt0) REVERT: F 601 LYS cc_start: 0.8666 (mttt) cc_final: 0.8183 (mttm) REVERT: F 634 GLU cc_start: 0.8557 (tt0) cc_final: 0.8163 (tp30) REVERT: F 644 ASN cc_start: 0.8330 (m110) cc_final: 0.7660 (m110) REVERT: G 26 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7503 (tm-30) REVERT: G 33 GLU cc_start: 0.8351 (mm-30) cc_final: 0.6411 (mp0) REVERT: G 36 TRP cc_start: 0.9131 (m100) cc_final: 0.8237 (m100) REVERT: G 39 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8228 (tm-30) REVERT: G 45 LEU cc_start: 0.7750 (mp) cc_final: 0.7509 (mp) REVERT: G 50 TRP cc_start: 0.9112 (p-90) cc_final: 0.8447 (p-90) REVERT: G 86 ASP cc_start: 0.8133 (m-30) cc_final: 0.7582 (t0) REVERT: G 89 THR cc_start: 0.9139 (m) cc_final: 0.8693 (p) REVERT: G 99 THR cc_start: 0.6008 (p) cc_final: 0.5744 (p) REVERT: G 108 LEU cc_start: 0.9279 (tp) cc_final: 0.8932 (tp) REVERT: J 33 MET cc_start: 0.8086 (ttm) cc_final: 0.7845 (mpp) REVERT: J 81 GLU cc_start: 0.8895 (tt0) cc_final: 0.8615 (tm-30) REVERT: J 96 GLU cc_start: 0.8459 (pt0) cc_final: 0.7800 (pt0) REVERT: I 33 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7043 (mp0) REVERT: I 36 TRP cc_start: 0.9135 (m100) cc_final: 0.8934 (m100) REVERT: I 50 TRP cc_start: 0.9169 (p-90) cc_final: 0.8736 (p-90) REVERT: I 89 THR cc_start: 0.9220 (m) cc_final: 0.8759 (p) REVERT: I 94 ARG cc_start: 0.7425 (ptm-80) cc_final: 0.6868 (ptt180) REVERT: I 99 THR cc_start: 0.6199 (p) cc_final: 0.5440 (t) REVERT: I 100 GLN cc_start: 0.8053 (tt0) cc_final: 0.7390 (tt0) REVERT: I 101 ASP cc_start: 0.7788 (t70) cc_final: 0.7429 (t70) REVERT: I 108 LEU cc_start: 0.9255 (tp) cc_final: 0.8917 (tp) REVERT: K 5 THR cc_start: 0.7506 (m) cc_final: 0.6855 (p) REVERT: K 81 GLU cc_start: 0.8816 (tt0) cc_final: 0.8489 (tm-30) REVERT: K 82 ASP cc_start: 0.8487 (m-30) cc_final: 0.8194 (m-30) REVERT: K 96 GLU cc_start: 0.8437 (pt0) cc_final: 0.8232 (pt0) outliers start: 5 outliers final: 3 residues processed: 635 average time/residue: 0.1519 time to fit residues: 150.5530 Evaluate side-chains 465 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 462 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 330 HIS A 374 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 70 GLN C 374 HIS E 575 GLN D 328 GLN D 330 HIS D 374 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098566 restraints weight = 43771.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101842 restraints weight = 27786.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104037 restraints weight = 20893.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105484 restraints weight = 17417.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106433 restraints weight = 15477.312| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21156 Z= 0.185 Angle : 0.769 17.871 28956 Z= 0.377 Chirality : 0.051 0.635 3582 Planarity : 0.005 0.063 3417 Dihedral : 5.019 18.307 2508 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.51 (0.17), residues: 2307 helix: 0.86 (0.23), residues: 450 sheet: 0.76 (0.19), residues: 738 loop : -0.08 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 192 TYR 0.038 0.002 TYR E 643 PHE 0.026 0.002 PHE A 233 TRP 0.017 0.002 TRP B 614 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20979) covalent geometry : angle 0.69182 / 0.36 (28458) SS BOND : bond 0.00414 / 0.28 ( 33) SS BOND : angle 1.09418 / 0.69 ( 66) hydrogen bonds : bond 0.05225 / 3.47 ( 735) hydrogen bonds : angle 5.86285 / 4.08 ( 1926) link_ALPHA1-2 : bond 0.01034 / 0.52 ( 3) link_ALPHA1-2 : angle 2.01893 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00795 / 0.38 ( 6) link_ALPHA1-3 : angle 1.57069 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00697 / 0.38 ( 6) link_ALPHA1-6 : angle 1.22822 / 0.61 ( 18) link_BETA1-4 : bond 0.00797 / 0.44 ( 48) link_BETA1-4 : angle 2.24194 / 1.58 ( 144) link_NAG-ASN : bond 0.00609 / 0.44 ( 81) link_NAG-ASN : angle 3.27869 / 2.03 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 567 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6620 (p-90) cc_final: 0.6138 (p-90) REVERT: A 78 ASP cc_start: 0.8192 (m-30) cc_final: 0.7478 (p0) REVERT: A 95 MET cc_start: 0.7860 (ptm) cc_final: 0.7620 (ptm) REVERT: A 292 VAL cc_start: 0.8567 (t) cc_final: 0.8084 (t) REVERT: A 333 ILE cc_start: 0.9233 (mt) cc_final: 0.8885 (tp) REVERT: A 414 ILE cc_start: 0.8784 (mt) cc_final: 0.8410 (mp) REVERT: B 584 GLU cc_start: 0.8769 (tt0) cc_final: 0.8439 (tt0) REVERT: B 634 GLU cc_start: 0.8680 (tt0) cc_final: 0.8332 (tt0) REVERT: B 644 ASN cc_start: 0.8113 (m110) cc_final: 0.7867 (m-40) REVERT: H 33 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6740 (mp0) REVERT: H 50 TRP cc_start: 0.9177 (p-90) cc_final: 0.8292 (p-90) REVERT: H 100 TRP cc_start: 0.8241 (m-10) cc_final: 0.7768 (m-10) REVERT: L 3 VAL cc_start: 0.8831 (t) cc_final: 0.8616 (t) REVERT: L 37 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8138 (pp30) REVERT: L 42 GLN cc_start: 0.8468 (tp40) cc_final: 0.8226 (tp-100) REVERT: L 78 MET cc_start: 0.8217 (tpp) cc_final: 0.7886 (tpp) REVERT: L 96 GLU cc_start: 0.8261 (pt0) cc_final: 0.7896 (pt0) REVERT: C 95 MET cc_start: 0.8110 (ptm) cc_final: 0.7897 (ptm) REVERT: C 217 TYR cc_start: 0.8076 (m-10) cc_final: 0.7628 (m-10) REVERT: C 430 VAL cc_start: 0.8659 (t) cc_final: 0.8409 (m) REVERT: E 539 VAL cc_start: 0.9291 (t) cc_final: 0.9083 (t) REVERT: E 540 GLN cc_start: 0.8573 (mm110) cc_final: 0.7693 (mm-40) REVERT: E 601 LYS cc_start: 0.8660 (mttt) cc_final: 0.8196 (mtmm) REVERT: E 616 ASN cc_start: 0.7992 (p0) cc_final: 0.7595 (p0) REVERT: E 634 GLU cc_start: 0.8416 (tt0) cc_final: 0.7988 (tp30) REVERT: E 638 TYR cc_start: 0.7125 (m-80) cc_final: 0.6890 (m-80) REVERT: E 639 THR cc_start: 0.9003 (m) cc_final: 0.8167 (p) REVERT: E 643 TYR cc_start: 0.8997 (m-80) cc_final: 0.8690 (m-80) REVERT: D 42 VAL cc_start: 0.8522 (p) cc_final: 0.8082 (p) REVERT: D 53 PHE cc_start: 0.8383 (p90) cc_final: 0.8003 (p90) REVERT: D 69 TRP cc_start: 0.6422 (p-90) cc_final: 0.5405 (p-90) REVERT: D 111 LEU cc_start: 0.8921 (tp) cc_final: 0.8455 (tp) REVERT: D 180 ASP cc_start: 0.8486 (m-30) cc_final: 0.8281 (m-30) REVERT: D 217 TYR cc_start: 0.8105 (m-80) cc_final: 0.7480 (m-80) REVERT: D 373 MET cc_start: 0.8459 (mtm) cc_final: 0.8237 (mtm) REVERT: F 540 GLN cc_start: 0.8539 (mm110) cc_final: 0.7497 (mm-40) REVERT: F 621 ASN cc_start: 0.8619 (t0) cc_final: 0.7938 (t0) REVERT: F 634 GLU cc_start: 0.8639 (tt0) cc_final: 0.8002 (tp30) REVERT: F 643 TYR cc_start: 0.8737 (m-80) cc_final: 0.8421 (m-80) REVERT: G 26 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7742 (tm-30) REVERT: G 36 TRP cc_start: 0.9163 (m100) cc_final: 0.8145 (m100) REVERT: G 39 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8002 (tm-30) REVERT: G 45 LEU cc_start: 0.7798 (mp) cc_final: 0.7551 (mp) REVERT: G 50 TRP cc_start: 0.9168 (p-90) cc_final: 0.8459 (p-90) REVERT: G 86 ASP cc_start: 0.8297 (m-30) cc_final: 0.7973 (t0) REVERT: G 89 THR cc_start: 0.9203 (m) cc_final: 0.8694 (p) REVERT: G 99 THR cc_start: 0.5892 (p) cc_final: 0.4979 (p) REVERT: G 102 LEU cc_start: 0.8975 (mt) cc_final: 0.8703 (mt) REVERT: G 108 LEU cc_start: 0.9207 (tp) cc_final: 0.8899 (tp) REVERT: J 3 VAL cc_start: 0.8799 (t) cc_final: 0.8420 (t) REVERT: I 28 ILE cc_start: 0.8284 (mt) cc_final: 0.8024 (mt) REVERT: I 46 GLU cc_start: 0.8255 (tp30) cc_final: 0.7085 (mm-30) REVERT: I 50 TRP cc_start: 0.9236 (p-90) cc_final: 0.8618 (p-90) REVERT: I 89 THR cc_start: 0.9162 (m) cc_final: 0.8729 (p) REVERT: I 99 THR cc_start: 0.6453 (p) cc_final: 0.5454 (t) REVERT: I 100 GLN cc_start: 0.7939 (tt0) cc_final: 0.7616 (tt0) REVERT: K 3 VAL cc_start: 0.8911 (t) cc_final: 0.8694 (t) REVERT: K 5 THR cc_start: 0.7652 (m) cc_final: 0.6875 (p) REVERT: K 37 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7997 (tm-30) REVERT: K 81 GLU cc_start: 0.8924 (tt0) cc_final: 0.8502 (tm-30) REVERT: K 82 ASP cc_start: 0.8489 (m-30) cc_final: 0.8039 (m-30) REVERT: K 103 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8172 (ttm110) outliers start: 5 outliers final: 0 residues processed: 571 average time/residue: 0.1498 time to fit residues: 132.7597 Evaluate side-chains 428 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 213 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 88 optimal weight: 0.0270 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 653 GLN B 656 ASN L 32 HIS L 37 GLN L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 330 HIS C 374 HIS E 653 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS D 374 HIS D 461 ASN F 575 GLN G 6 GLN J 32 HIS J 70 GLN J 90 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099179 restraints weight = 43305.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102459 restraints weight = 28098.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104670 restraints weight = 21372.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106116 restraints weight = 17948.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107143 restraints weight = 15999.158| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21156 Z= 0.144 Angle : 0.691 14.710 28956 Z= 0.340 Chirality : 0.048 0.530 3582 Planarity : 0.005 0.058 3417 Dihedral : 4.891 25.378 2508 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.39 % Allowed : 2.03 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.34 (0.17), residues: 2307 helix: 0.85 (0.24), residues: 450 sheet: 0.60 (0.19), residues: 753 loop : -0.20 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 38 TYR 0.031 0.002 TYR E 643 PHE 0.022 0.002 PHE C 233 TRP 0.024 0.002 TRP F 610 HIS 0.008 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (20979) covalent geometry : angle 0.63462 / 0.33 (28458) SS BOND : bond 0.00367 / 0.25 ( 33) SS BOND : angle 1.02837 / 0.65 ( 66) hydrogen bonds : bond 0.04555 / 3.03 ( 735) hydrogen bonds : angle 5.57394 / 3.88 ( 1926) link_ALPHA1-2 : bond 0.01019 / 0.51 ( 3) link_ALPHA1-2 : angle 2.06079 / 1.06 ( 9) link_ALPHA1-3 : bond 0.00692 / 0.35 ( 6) link_ALPHA1-3 : angle 1.46811 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00616 / 0.33 ( 6) link_ALPHA1-6 : angle 1.30858 / 0.65 ( 18) link_BETA1-4 : bond 0.00735 / 0.40 ( 48) link_BETA1-4 : angle 1.84661 / 1.32 ( 144) link_NAG-ASN : bond 0.00531 / 0.35 ( 81) link_NAG-ASN : angle 2.63017 / 1.64 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 527 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6462 (p-90) cc_final: 0.5923 (p-90) REVERT: A 78 ASP cc_start: 0.8175 (m-30) cc_final: 0.7490 (p0) REVERT: A 95 MET cc_start: 0.7865 (ptm) cc_final: 0.7610 (ptm) REVERT: A 333 ILE cc_start: 0.9227 (mt) cc_final: 0.8888 (tp) REVERT: A 414 ILE cc_start: 0.8754 (mt) cc_final: 0.8346 (mp) REVERT: B 584 GLU cc_start: 0.8763 (tt0) cc_final: 0.8515 (tt0) REVERT: B 634 GLU cc_start: 0.8731 (tt0) cc_final: 0.8437 (tt0) REVERT: B 653 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: H 33 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6903 (mt-10) REVERT: H 50 TRP cc_start: 0.9202 (p-90) cc_final: 0.8381 (p-90) REVERT: H 99 THR cc_start: 0.6228 (t) cc_final: 0.5179 (m) REVERT: H 100 GLN cc_start: 0.7550 (tt0) cc_final: 0.7283 (tm-30) REVERT: H 100 TRP cc_start: 0.8218 (m-10) cc_final: 0.7847 (m-10) REVERT: L 5 THR cc_start: 0.8032 (m) cc_final: 0.7413 (p) REVERT: L 17 GLU cc_start: 0.8221 (pt0) cc_final: 0.7669 (pm20) REVERT: L 42 GLN cc_start: 0.8464 (tp40) cc_final: 0.8175 (tp-100) REVERT: L 46 LEU cc_start: 0.8248 (pt) cc_final: 0.7840 (pp) REVERT: L 47 LEU cc_start: 0.8541 (mt) cc_final: 0.8335 (mm) REVERT: L 60 ASP cc_start: 0.8511 (t0) cc_final: 0.8262 (t70) REVERT: L 86 TYR cc_start: 0.8197 (m-80) cc_final: 0.7114 (m-80) REVERT: L 96 GLU cc_start: 0.8266 (pt0) cc_final: 0.7880 (pt0) REVERT: C 104 MET cc_start: 0.8631 (tpp) cc_final: 0.8367 (tpp) REVERT: C 373 MET cc_start: 0.8545 (mtm) cc_final: 0.8318 (mtm) REVERT: C 430 VAL cc_start: 0.8708 (t) cc_final: 0.8485 (m) REVERT: E 540 GLN cc_start: 0.8546 (mm110) cc_final: 0.7630 (mm-40) REVERT: E 601 LYS cc_start: 0.8537 (mttt) cc_final: 0.8017 (mtmm) REVERT: E 634 GLU cc_start: 0.8471 (tt0) cc_final: 0.7981 (tp30) REVERT: E 638 TYR cc_start: 0.7158 (m-80) cc_final: 0.6829 (m-80) REVERT: E 639 THR cc_start: 0.9064 (m) cc_final: 0.8294 (p) REVERT: E 643 TYR cc_start: 0.9078 (m-80) cc_final: 0.8843 (m-80) REVERT: E 648 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7568 (tm-30) REVERT: E 653 GLN cc_start: 0.8481 (tm130) cc_final: 0.8258 (tm-30) REVERT: D 53 PHE cc_start: 0.8443 (p90) cc_final: 0.8115 (p90) REVERT: D 69 TRP cc_start: 0.6342 (p-90) cc_final: 0.5231 (p-90) REVERT: D 111 LEU cc_start: 0.8935 (tp) cc_final: 0.8472 (tp) REVERT: D 165 VAL cc_start: 0.7546 (m) cc_final: 0.6758 (m) REVERT: D 180 ASP cc_start: 0.8488 (m-30) cc_final: 0.8259 (m-30) REVERT: D 217 TYR cc_start: 0.8003 (m-80) cc_final: 0.7428 (m-80) REVERT: D 373 MET cc_start: 0.8563 (mtm) cc_final: 0.8281 (mtm) REVERT: F 621 ASN cc_start: 0.8650 (t0) cc_final: 0.8240 (t0) REVERT: F 626 MET cc_start: 0.7233 (ttm) cc_final: 0.6845 (ttm) REVERT: F 634 GLU cc_start: 0.8571 (tt0) cc_final: 0.8027 (tp30) REVERT: G 26 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7436 (tm-30) REVERT: G 36 TRP cc_start: 0.9113 (m100) cc_final: 0.8178 (m100) REVERT: G 47 TRP cc_start: 0.8728 (t60) cc_final: 0.8018 (t60) REVERT: G 50 TRP cc_start: 0.9144 (p-90) cc_final: 0.8502 (p-90) REVERT: G 81 ASP cc_start: 0.8447 (m-30) cc_final: 0.7659 (t0) REVERT: G 86 ASP cc_start: 0.8351 (m-30) cc_final: 0.7775 (t0) REVERT: G 96 LYS cc_start: 0.7128 (pttp) cc_final: 0.6355 (ptpp) REVERT: G 99 THR cc_start: 0.6054 (p) cc_final: 0.4842 (t) REVERT: G 100 TRP cc_start: 0.7653 (m-10) cc_final: 0.6995 (m-10) REVERT: G 101 ASP cc_start: 0.8119 (t0) cc_final: 0.7771 (t0) REVERT: G 102 LEU cc_start: 0.8878 (mt) cc_final: 0.8674 (mt) REVERT: G 108 LEU cc_start: 0.9153 (tp) cc_final: 0.8894 (tp) REVERT: J 5 THR cc_start: 0.7632 (m) cc_final: 0.6925 (p) REVERT: J 22 SER cc_start: 0.8808 (m) cc_final: 0.8250 (p) REVERT: J 34 THR cc_start: 0.9011 (m) cc_final: 0.8611 (p) REVERT: J 60 ASP cc_start: 0.8046 (t0) cc_final: 0.7215 (t0) REVERT: J 96 GLU cc_start: 0.8404 (pt0) cc_final: 0.6969 (pt0) REVERT: I 99 THR cc_start: 0.6762 (p) cc_final: 0.5625 (t) REVERT: K 5 THR cc_start: 0.7463 (m) cc_final: 0.6733 (p) REVERT: K 17 GLU cc_start: 0.8685 (pt0) cc_final: 0.7949 (pm20) REVERT: K 37 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7418 (tm-30) REVERT: K 65 SER cc_start: 0.9147 (t) cc_final: 0.8594 (t) REVERT: K 81 GLU cc_start: 0.9164 (tt0) cc_final: 0.8642 (tm-30) REVERT: K 82 ASP cc_start: 0.8527 (m-30) cc_final: 0.7851 (m-30) REVERT: K 103 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8163 (ttm110) outliers start: 8 outliers final: 1 residues processed: 531 average time/residue: 0.1410 time to fit residues: 119.1697 Evaluate side-chains 428 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 173 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 214 optimal weight: 0.0060 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN C 203 GLN E 575 GLN D 203 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN J 32 HIS J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096042 restraints weight = 43264.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099101 restraints weight = 28189.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101161 restraints weight = 21604.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102544 restraints weight = 18232.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103474 restraints weight = 16289.634| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21156 Z= 0.166 Angle : 0.679 11.042 28956 Z= 0.338 Chirality : 0.046 0.292 3582 Planarity : 0.005 0.064 3417 Dihedral : 4.838 28.232 2508 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.24 % Allowed : 2.23 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.17), residues: 2307 helix: 0.93 (0.24), residues: 453 sheet: 0.50 (0.19), residues: 771 loop : -0.22 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 103 TYR 0.023 0.002 TYR E 643 PHE 0.021 0.002 PHE C 233 TRP 0.030 0.002 TRP I 36 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (20979) covalent geometry : angle 0.64006 / 0.33 (28458) SS BOND : bond 0.00386 / 0.26 ( 33) SS BOND : angle 1.17081 / 0.72 ( 66) hydrogen bonds : bond 0.04683 / 3.07 ( 735) hydrogen bonds : angle 5.40401 / 3.77 ( 1926) link_ALPHA1-2 : bond 0.00883 / 0.44 ( 3) link_ALPHA1-2 : angle 1.99965 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00522 / 0.23 ( 6) link_ALPHA1-3 : angle 1.63619 / 0.85 ( 18) link_ALPHA1-6 : bond 0.00655 / 0.36 ( 6) link_ALPHA1-6 : angle 1.26354 / 0.63 ( 18) link_BETA1-4 : bond 0.00615 / 0.33 ( 48) link_BETA1-4 : angle 1.67610 / 1.21 ( 144) link_NAG-ASN : bond 0.00346 / 0.21 ( 81) link_NAG-ASN : angle 2.10343 / 1.37 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 495 time to evaluate : 0.725 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 69 TRP cc_start: 0.6345 (p-90) cc_final: 0.5392 (p-90) REVERT: A 78 ASP cc_start: 0.8172 (m-30) cc_final: 0.7533 (p0) REVERT: A 95 MET cc_start: 0.7968 (ptm) cc_final: 0.7664 (ptm) REVERT: A 111 LEU cc_start: 0.8920 (mt) cc_final: 0.8674 (mt) REVERT: A 292 VAL cc_start: 0.8806 (t) cc_final: 0.8394 (t) REVERT: A 414 ILE cc_start: 0.8758 (mt) cc_final: 0.8399 (mp) REVERT: B 584 GLU cc_start: 0.8875 (tt0) cc_final: 0.8290 (tp30) REVERT: B 634 GLU cc_start: 0.8716 (tt0) cc_final: 0.8380 (tt0) REVERT: H 31 ARG cc_start: 0.8353 (ptp-110) cc_final: 0.7035 (tpm170) REVERT: H 50 TRP cc_start: 0.9239 (p-90) cc_final: 0.8472 (p-90) REVERT: H 89 THR cc_start: 0.9272 (m) cc_final: 0.8853 (p) REVERT: H 108 LEU cc_start: 0.9369 (tp) cc_final: 0.9135 (tp) REVERT: L 5 THR cc_start: 0.8058 (m) cc_final: 0.7431 (p) REVERT: L 17 GLU cc_start: 0.8229 (pt0) cc_final: 0.7725 (pm20) REVERT: L 42 GLN cc_start: 0.8447 (tp40) cc_final: 0.8123 (tp-100) REVERT: L 46 LEU cc_start: 0.8156 (pt) cc_final: 0.7867 (pp) REVERT: L 47 LEU cc_start: 0.8500 (mt) cc_final: 0.8281 (mm) REVERT: C 104 MET cc_start: 0.8051 (tpp) cc_final: 0.7235 (tpp) REVERT: C 348 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8076 (tptt) REVERT: C 373 MET cc_start: 0.8779 (mtm) cc_final: 0.8534 (mtm) REVERT: C 430 VAL cc_start: 0.8769 (t) cc_final: 0.8559 (m) REVERT: E 539 VAL cc_start: 0.9180 (t) cc_final: 0.8978 (t) REVERT: E 540 GLN cc_start: 0.8765 (mm110) cc_final: 0.7689 (mm-40) REVERT: E 584 GLU cc_start: 0.8909 (tt0) cc_final: 0.8330 (tp30) REVERT: E 601 LYS cc_start: 0.8613 (mttt) cc_final: 0.8152 (mtmm) REVERT: E 616 ASN cc_start: 0.8027 (p0) cc_final: 0.7741 (p0) REVERT: E 634 GLU cc_start: 0.8532 (tt0) cc_final: 0.7962 (tp30) REVERT: E 639 THR cc_start: 0.9128 (m) cc_final: 0.8623 (p) REVERT: E 648 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 203 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8918 (pp30) REVERT: D 373 MET cc_start: 0.8629 (mtm) cc_final: 0.8356 (mtm) REVERT: D 414 ILE cc_start: 0.8699 (mt) cc_final: 0.8432 (tp) REVERT: F 621 ASN cc_start: 0.8425 (t0) cc_final: 0.8070 (t0) REVERT: F 634 GLU cc_start: 0.8572 (tt0) cc_final: 0.8012 (tp30) REVERT: G 26 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7424 (tm-30) REVERT: G 31 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8229 (ttm110) REVERT: G 36 TRP cc_start: 0.9149 (m100) cc_final: 0.8147 (m100) REVERT: G 39 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8254 (tm-30) REVERT: G 46 GLU cc_start: 0.8465 (tp30) cc_final: 0.7173 (mm-30) REVERT: G 47 TRP cc_start: 0.8757 (t60) cc_final: 0.7739 (t60) REVERT: G 50 TRP cc_start: 0.9248 (p-90) cc_final: 0.8861 (p-90) REVERT: G 86 ASP cc_start: 0.8373 (m-30) cc_final: 0.8090 (m-30) REVERT: G 89 THR cc_start: 0.9242 (m) cc_final: 0.8565 (p) REVERT: G 98 TYR cc_start: 0.4331 (t80) cc_final: 0.3953 (t80) REVERT: G 108 LEU cc_start: 0.9057 (tp) cc_final: 0.8786 (tp) REVERT: J 5 THR cc_start: 0.7816 (m) cc_final: 0.7138 (p) REVERT: J 22 SER cc_start: 0.8514 (m) cc_final: 0.7958 (p) REVERT: J 34 THR cc_start: 0.9135 (m) cc_final: 0.8607 (p) REVERT: J 42 GLN cc_start: 0.8286 (tp40) cc_final: 0.8028 (tp-100) REVERT: J 96 GLU cc_start: 0.8577 (pt0) cc_final: 0.7377 (pt0) REVERT: I 89 THR cc_start: 0.9151 (m) cc_final: 0.8655 (p) REVERT: I 98 TYR cc_start: 0.5224 (t80) cc_final: 0.4576 (t80) REVERT: I 108 LEU cc_start: 0.9318 (tp) cc_final: 0.9018 (tp) REVERT: K 5 THR cc_start: 0.7568 (m) cc_final: 0.6822 (p) REVERT: K 65 SER cc_start: 0.9124 (t) cc_final: 0.8633 (t) REVERT: K 81 GLU cc_start: 0.9231 (tt0) cc_final: 0.8686 (tm-30) REVERT: K 82 ASP cc_start: 0.8618 (m-30) cc_final: 0.7885 (m-30) outliers start: 5 outliers final: 0 residues processed: 498 average time/residue: 0.1380 time to fit residues: 109.9612 Evaluate side-chains 401 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 104 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN J 32 HIS J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.124504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095048 restraints weight = 43437.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098293 restraints weight = 27598.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100457 restraints weight = 20862.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101874 restraints weight = 17484.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102825 restraints weight = 15595.806| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21156 Z= 0.157 Angle : 0.685 25.579 28956 Z= 0.336 Chirality : 0.047 0.619 3582 Planarity : 0.005 0.068 3417 Dihedral : 4.782 25.146 2508 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.15 % Allowed : 1.16 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.28 (0.17), residues: 2307 helix: 1.13 (0.25), residues: 432 sheet: 0.45 (0.19), residues: 756 loop : -0.29 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 103 TYR 0.014 0.001 TYR C 217 PHE 0.031 0.002 PHE H 97 TRP 0.021 0.001 TRP I 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (20979) covalent geometry : angle 0.62898 / 0.32 (28458) SS BOND : bond 0.00387 / 0.26 ( 33) SS BOND : angle 1.36646 / 0.94 ( 66) hydrogen bonds : bond 0.04540 / 3.02 ( 735) hydrogen bonds : angle 5.39503 / 3.77 ( 1926) link_ALPHA1-2 : bond 0.00888 / 0.45 ( 3) link_ALPHA1-2 : angle 1.99140 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00634 / 0.29 ( 6) link_ALPHA1-3 : angle 1.31472 / 0.64 ( 18) link_ALPHA1-6 : bond 0.00603 / 0.33 ( 6) link_ALPHA1-6 : angle 1.30259 / 0.65 ( 18) link_BETA1-4 : bond 0.00639 / 0.31 ( 48) link_BETA1-4 : angle 1.64457 / 1.18 ( 144) link_NAG-ASN : bond 0.00475 / 0.35 ( 81) link_NAG-ASN : angle 2.65942 / 1.68 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 505 time to evaluate : 0.760 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: A 78 ASP cc_start: 0.8190 (m-30) cc_final: 0.7513 (p0) REVERT: A 104 MET cc_start: 0.8421 (tpp) cc_final: 0.7598 (tpp) REVERT: A 425 ASN cc_start: 0.7801 (t0) cc_final: 0.7569 (t0) REVERT: B 530 MET cc_start: 0.8903 (mmm) cc_final: 0.8682 (mmm) REVERT: B 543 GLN cc_start: 0.8401 (mt0) cc_final: 0.8134 (mt0) REVERT: B 584 GLU cc_start: 0.8913 (tt0) cc_final: 0.8272 (tp30) REVERT: B 634 GLU cc_start: 0.8757 (tt0) cc_final: 0.8418 (tt0) REVERT: H 31 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7057 (tpm170) REVERT: H 50 TRP cc_start: 0.9315 (p-90) cc_final: 0.8686 (p-90) REVERT: H 89 THR cc_start: 0.9288 (m) cc_final: 0.8858 (p) REVERT: H 99 THR cc_start: 0.6226 (t) cc_final: 0.5514 (t) REVERT: H 108 LEU cc_start: 0.9358 (tp) cc_final: 0.9125 (tp) REVERT: L 5 THR cc_start: 0.8047 (m) cc_final: 0.7431 (p) REVERT: L 42 GLN cc_start: 0.8407 (tp40) cc_final: 0.8053 (tp-100) REVERT: L 46 LEU cc_start: 0.8166 (pt) cc_final: 0.7851 (pp) REVERT: L 66 GLN cc_start: 0.8061 (pt0) cc_final: 0.7829 (pt0) REVERT: C 242 VAL cc_start: 0.9169 (m) cc_final: 0.8928 (p) REVERT: C 333 ILE cc_start: 0.9127 (mm) cc_final: 0.8867 (tp) REVERT: C 373 MET cc_start: 0.8828 (mtm) cc_final: 0.8592 (mtm) REVERT: C 430 VAL cc_start: 0.8754 (t) cc_final: 0.8513 (m) REVERT: E 540 GLN cc_start: 0.8727 (mm110) cc_final: 0.7724 (mm-40) REVERT: E 543 GLN cc_start: 0.8473 (mt0) cc_final: 0.8248 (mt0) REVERT: E 584 GLU cc_start: 0.8888 (tt0) cc_final: 0.8395 (tp30) REVERT: E 601 LYS cc_start: 0.8695 (mttt) cc_final: 0.8305 (mtmm) REVERT: E 616 ASN cc_start: 0.8133 (p0) cc_final: 0.7908 (p0) REVERT: E 634 GLU cc_start: 0.8704 (tt0) cc_final: 0.8169 (tp30) REVERT: E 648 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 53 PHE cc_start: 0.8368 (p90) cc_final: 0.7988 (p90) REVERT: D 203 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8606 (tm-30) REVERT: D 373 MET cc_start: 0.8744 (mtm) cc_final: 0.8425 (mtm) REVERT: D 395 TRP cc_start: 0.7241 (m100) cc_final: 0.7033 (m100) REVERT: D 466 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7716 (mp0) REVERT: F 545 LEU cc_start: 0.8246 (tt) cc_final: 0.7961 (tp) REVERT: F 621 ASN cc_start: 0.8535 (t0) cc_final: 0.8135 (t0) REVERT: F 626 MET cc_start: 0.7192 (ttm) cc_final: 0.6925 (ttm) REVERT: F 634 GLU cc_start: 0.8523 (tt0) cc_final: 0.8315 (tm-30) REVERT: G 26 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7568 (tm-30) REVERT: G 36 TRP cc_start: 0.9192 (m100) cc_final: 0.8144 (m100) REVERT: G 39 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8207 (tm-30) REVERT: G 46 GLU cc_start: 0.8382 (tp30) cc_final: 0.8178 (tp30) REVERT: G 47 TRP cc_start: 0.8801 (t60) cc_final: 0.8137 (t60) REVERT: G 50 TRP cc_start: 0.9196 (p-90) cc_final: 0.8767 (p-90) REVERT: G 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7754 (t0) REVERT: G 82 LEU cc_start: 0.9266 (tp) cc_final: 0.9024 (tp) REVERT: G 86 ASP cc_start: 0.8346 (m-30) cc_final: 0.7913 (m-30) REVERT: G 89 THR cc_start: 0.9231 (m) cc_final: 0.8669 (p) REVERT: G 95 GLN cc_start: 0.7942 (tt0) cc_final: 0.7426 (tm-30) REVERT: G 98 TYR cc_start: 0.4432 (t80) cc_final: 0.4154 (t80) REVERT: G 99 THR cc_start: 0.6283 (t) cc_final: 0.5752 (t) REVERT: G 108 LEU cc_start: 0.9009 (tp) cc_final: 0.8745 (tp) REVERT: J 5 THR cc_start: 0.7684 (m) cc_final: 0.6987 (p) REVERT: J 22 SER cc_start: 0.8515 (m) cc_final: 0.8076 (p) REVERT: J 34 THR cc_start: 0.9133 (m) cc_final: 0.8635 (p) REVERT: J 42 GLN cc_start: 0.8224 (tp40) cc_final: 0.7915 (tp-100) REVERT: J 96 GLU cc_start: 0.8630 (pt0) cc_final: 0.7627 (pt0) REVERT: I 89 THR cc_start: 0.9125 (m) cc_final: 0.8640 (p) REVERT: I 108 LEU cc_start: 0.9303 (tp) cc_final: 0.9030 (tp) REVERT: K 5 THR cc_start: 0.7619 (m) cc_final: 0.6925 (p) REVERT: K 42 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8437 (tp-100) REVERT: K 82 ASP cc_start: 0.8712 (m-30) cc_final: 0.8075 (m-30) outliers start: 3 outliers final: 0 residues processed: 506 average time/residue: 0.1406 time to fit residues: 113.0916 Evaluate side-chains 407 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN L 70 GLN E 658 GLN G 100BGLN J 32 HIS J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096955 restraints weight = 43345.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100253 restraints weight = 27248.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102497 restraints weight = 20457.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103930 restraints weight = 17003.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104775 restraints weight = 15133.112| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21156 Z= 0.132 Angle : 0.669 18.826 28956 Z= 0.331 Chirality : 0.047 0.636 3582 Planarity : 0.005 0.064 3417 Dihedral : 4.793 27.211 2508 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 0.15 % Allowed : 1.21 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2307 helix: 1.12 (0.25), residues: 432 sheet: 0.43 (0.19), residues: 750 loop : -0.43 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 31 TYR 0.012 0.001 TYR B 643 PHE 0.020 0.002 PHE G 97 TRP 0.024 0.001 TRP H 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20979) covalent geometry : angle 0.62643 / 0.32 (28458) SS BOND : bond 0.00326 / 0.21 ( 33) SS BOND : angle 1.06983 / 0.71 ( 66) hydrogen bonds : bond 0.04214 / 2.82 ( 735) hydrogen bonds : angle 5.25269 / 3.67 ( 1926) link_ALPHA1-2 : bond 0.00910 / 0.46 ( 3) link_ALPHA1-2 : angle 1.98378 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00681 / 0.33 ( 6) link_ALPHA1-3 : angle 1.29764 / 0.64 ( 18) link_ALPHA1-6 : bond 0.00544 / 0.30 ( 6) link_ALPHA1-6 : angle 1.36369 / 0.68 ( 18) link_BETA1-4 : bond 0.00577 / 0.30 ( 48) link_BETA1-4 : angle 1.54442 / 1.11 ( 144) link_NAG-ASN : bond 0.00402 / 0.28 ( 81) link_NAG-ASN : angle 2.30650 / 1.46 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 0.791 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 78 ASP cc_start: 0.8230 (m-30) cc_final: 0.7483 (p0) REVERT: A 104 MET cc_start: 0.8472 (tpp) cc_final: 0.8182 (tpp) REVERT: A 414 ILE cc_start: 0.8570 (mt) cc_final: 0.8270 (tp) REVERT: A 425 ASN cc_start: 0.7755 (t0) cc_final: 0.7476 (t0) REVERT: B 584 GLU cc_start: 0.8871 (tt0) cc_final: 0.8287 (tp30) REVERT: B 634 GLU cc_start: 0.8763 (tt0) cc_final: 0.8318 (tt0) REVERT: B 649 SER cc_start: 0.9105 (p) cc_final: 0.8517 (p) REVERT: H 31 ARG cc_start: 0.8467 (ptp-110) cc_final: 0.6973 (tpm170) REVERT: H 50 TRP cc_start: 0.9173 (p-90) cc_final: 0.8557 (p-90) REVERT: H 89 THR cc_start: 0.9274 (m) cc_final: 0.8822 (p) REVERT: H 99 THR cc_start: 0.6072 (t) cc_final: 0.4717 (t) REVERT: H 100 GLN cc_start: 0.6668 (tm-30) cc_final: 0.6303 (tm-30) REVERT: H 100 TYR cc_start: 0.5006 (m-80) cc_final: 0.4737 (m-80) REVERT: H 108 LEU cc_start: 0.9319 (tp) cc_final: 0.9076 (tp) REVERT: L 5 THR cc_start: 0.8141 (m) cc_final: 0.7569 (p) REVERT: L 42 GLN cc_start: 0.8345 (tp40) cc_final: 0.7980 (tp-100) REVERT: L 46 LEU cc_start: 0.8371 (pt) cc_final: 0.8145 (pp) REVERT: L 66 GLN cc_start: 0.8203 (pt0) cc_final: 0.7932 (pt0) REVERT: C 111 LEU cc_start: 0.8764 (tt) cc_final: 0.8538 (tt) REVERT: C 242 VAL cc_start: 0.9187 (m) cc_final: 0.8944 (p) REVERT: C 373 MET cc_start: 0.8818 (mtm) cc_final: 0.8593 (mtm) REVERT: C 430 VAL cc_start: 0.8735 (t) cc_final: 0.8495 (m) REVERT: E 540 GLN cc_start: 0.8529 (mm110) cc_final: 0.7810 (mm-40) REVERT: E 584 GLU cc_start: 0.8709 (tt0) cc_final: 0.8437 (tp30) REVERT: E 601 LYS cc_start: 0.8667 (mttt) cc_final: 0.8337 (mtmm) REVERT: E 616 ASN cc_start: 0.8087 (p0) cc_final: 0.7845 (p0) REVERT: E 634 GLU cc_start: 0.8712 (tt0) cc_final: 0.8177 (tp30) REVERT: E 648 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 53 PHE cc_start: 0.8308 (p90) cc_final: 0.7914 (p90) REVERT: D 203 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8574 (tm-30) REVERT: D 348 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8835 (tptt) REVERT: D 373 MET cc_start: 0.8770 (mtm) cc_final: 0.8447 (mtm) REVERT: D 395 TRP cc_start: 0.7199 (m100) cc_final: 0.6992 (m100) REVERT: D 466 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7875 (mp0) REVERT: F 621 ASN cc_start: 0.8406 (t0) cc_final: 0.8031 (t0) REVERT: F 626 MET cc_start: 0.7486 (ttm) cc_final: 0.7236 (ttm) REVERT: F 634 GLU cc_start: 0.8605 (tt0) cc_final: 0.8254 (tm-30) REVERT: F 643 TYR cc_start: 0.8995 (m-80) cc_final: 0.8498 (m-80) REVERT: F 649 SER cc_start: 0.9036 (p) cc_final: 0.8612 (p) REVERT: G 36 TRP cc_start: 0.9128 (m100) cc_final: 0.8095 (m100) REVERT: G 39 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8235 (tm-30) REVERT: G 47 TRP cc_start: 0.8765 (t60) cc_final: 0.8232 (t60) REVERT: G 50 TRP cc_start: 0.9278 (p-90) cc_final: 0.8793 (p-90) REVERT: G 65 GLN cc_start: 0.8822 (tt0) cc_final: 0.8618 (mt0) REVERT: G 72 ASP cc_start: 0.8160 (t0) cc_final: 0.7770 (t0) REVERT: G 86 ASP cc_start: 0.8304 (m-30) cc_final: 0.7855 (m-30) REVERT: G 89 THR cc_start: 0.9239 (m) cc_final: 0.8565 (p) REVERT: G 95 GLN cc_start: 0.7722 (tt0) cc_final: 0.7298 (tm-30) REVERT: G 99 THR cc_start: 0.5520 (t) cc_final: 0.5137 (p) REVERT: G 108 LEU cc_start: 0.8885 (tp) cc_final: 0.8672 (tp) REVERT: J 5 THR cc_start: 0.7607 (m) cc_final: 0.6949 (p) REVERT: J 34 THR cc_start: 0.9027 (m) cc_final: 0.8523 (p) REVERT: J 42 GLN cc_start: 0.8154 (tp40) cc_final: 0.7836 (tp-100) REVERT: J 96 GLU cc_start: 0.8606 (pt0) cc_final: 0.7597 (pt0) REVERT: I 50 TRP cc_start: 0.9102 (p-90) cc_final: 0.8459 (p-90) REVERT: I 75 LEU cc_start: 0.7901 (mt) cc_final: 0.7491 (tp) REVERT: I 89 THR cc_start: 0.9113 (m) cc_final: 0.8630 (p) REVERT: I 98 TYR cc_start: 0.4837 (t80) cc_final: 0.4482 (t80) REVERT: K 5 THR cc_start: 0.7560 (m) cc_final: 0.6887 (p) REVERT: K 42 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8321 (tp-100) REVERT: K 65 SER cc_start: 0.9315 (t) cc_final: 0.9049 (t) outliers start: 3 outliers final: 0 residues processed: 508 average time/residue: 0.1353 time to fit residues: 108.8149 Evaluate side-chains 406 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 54 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN J 32 HIS J 70 GLN I 57 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.121882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093738 restraints weight = 44223.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096826 restraints weight = 28129.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098918 restraints weight = 21257.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100300 restraints weight = 17794.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101219 restraints weight = 15828.288| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21156 Z= 0.184 Angle : 0.716 16.843 28956 Z= 0.356 Chirality : 0.048 0.558 3582 Planarity : 0.005 0.072 3417 Dihedral : 4.971 32.930 2508 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 0.53 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 2307 helix: 1.03 (0.25), residues: 435 sheet: 0.49 (0.19), residues: 729 loop : -0.51 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 31 TYR 0.015 0.002 TYR C 217 PHE 0.022 0.002 PHE K 62 TRP 0.037 0.002 TRP H 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (20979) covalent geometry : angle 0.67533 / 0.35 (28458) SS BOND : bond 0.00348 / 0.23 ( 33) SS BOND : angle 1.27099 / 0.77 ( 66) hydrogen bonds : bond 0.04736 / 3.18 ( 735) hydrogen bonds : angle 5.33635 / 3.74 ( 1926) link_ALPHA1-2 : bond 0.00755 / 0.38 ( 3) link_ALPHA1-2 : angle 1.90629 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00571 / 0.27 ( 6) link_ALPHA1-3 : angle 1.32928 / 0.65 ( 18) link_ALPHA1-6 : bond 0.00597 / 0.33 ( 6) link_ALPHA1-6 : angle 1.28407 / 0.64 ( 18) link_BETA1-4 : bond 0.00548 / 0.27 ( 48) link_BETA1-4 : angle 1.56124 / 1.13 ( 144) link_NAG-ASN : bond 0.00366 / 0.24 ( 81) link_NAG-ASN : angle 2.31371 / 1.55 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 482 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8228 (m-30) cc_final: 0.7625 (p0) REVERT: A 95 MET cc_start: 0.7953 (ptm) cc_final: 0.7573 (ppp) REVERT: A 425 ASN cc_start: 0.7934 (t0) cc_final: 0.7628 (t0) REVERT: B 584 GLU cc_start: 0.8948 (tt0) cc_final: 0.8396 (tp30) REVERT: B 634 GLU cc_start: 0.8661 (tt0) cc_final: 0.8258 (tt0) REVERT: H 31 ARG cc_start: 0.8550 (ptp-110) cc_final: 0.7057 (tpm170) REVERT: H 89 THR cc_start: 0.9310 (m) cc_final: 0.8847 (p) REVERT: H 95 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7929 (tm-30) REVERT: H 99 THR cc_start: 0.6236 (t) cc_final: 0.5660 (t) REVERT: H 108 LEU cc_start: 0.9367 (tp) cc_final: 0.9064 (tp) REVERT: L 42 GLN cc_start: 0.8349 (tp40) cc_final: 0.8012 (tp-100) REVERT: L 46 LEU cc_start: 0.8323 (pt) cc_final: 0.8008 (pp) REVERT: L 60 ASP cc_start: 0.7773 (m-30) cc_final: 0.7414 (m-30) REVERT: L 66 GLN cc_start: 0.8218 (pt0) cc_final: 0.7667 (pt0) REVERT: C 373 MET cc_start: 0.8885 (mtm) cc_final: 0.8613 (mtm) REVERT: C 430 VAL cc_start: 0.8917 (t) cc_final: 0.8661 (m) REVERT: E 540 GLN cc_start: 0.8623 (mm110) cc_final: 0.7984 (mm-40) REVERT: E 584 GLU cc_start: 0.8770 (tt0) cc_final: 0.8487 (tp30) REVERT: E 601 LYS cc_start: 0.8863 (mttt) cc_final: 0.8569 (mtmm) REVERT: E 616 ASN cc_start: 0.8071 (p0) cc_final: 0.7810 (p0) REVERT: E 621 ASN cc_start: 0.8414 (p0) cc_final: 0.8180 (t0) REVERT: E 648 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7708 (tm-30) REVERT: E 656 ASN cc_start: 0.9363 (p0) cc_final: 0.9160 (p0) REVERT: D 53 PHE cc_start: 0.8455 (p90) cc_final: 0.8125 (p90) REVERT: D 95 MET cc_start: 0.7914 (ptm) cc_final: 0.7620 (ppp) REVERT: D 203 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 348 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8931 (tptt) REVERT: D 373 MET cc_start: 0.8853 (mtm) cc_final: 0.8552 (mtm) REVERT: D 466 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7904 (mp0) REVERT: F 621 ASN cc_start: 0.8254 (t0) cc_final: 0.7921 (t0) REVERT: G 36 TRP cc_start: 0.9179 (m100) cc_final: 0.8206 (m100) REVERT: G 39 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 47 TRP cc_start: 0.8903 (t60) cc_final: 0.8451 (t60) REVERT: G 72 ASP cc_start: 0.8407 (t0) cc_final: 0.7981 (t0) REVERT: G 86 ASP cc_start: 0.8387 (m-30) cc_final: 0.7944 (m-30) REVERT: G 95 GLN cc_start: 0.7766 (tt0) cc_final: 0.7471 (tm-30) REVERT: G 99 THR cc_start: 0.6124 (t) cc_final: 0.5841 (t) REVERT: G 108 LEU cc_start: 0.8929 (tp) cc_final: 0.8719 (tp) REVERT: J 34 THR cc_start: 0.9113 (m) cc_final: 0.8657 (p) REVERT: J 42 GLN cc_start: 0.8154 (tp40) cc_final: 0.7817 (tp-100) REVERT: J 96 GLU cc_start: 0.8615 (pt0) cc_final: 0.7983 (pt0) REVERT: I 89 THR cc_start: 0.9045 (m) cc_final: 0.8627 (p) REVERT: I 99 THR cc_start: 0.6882 (t) cc_final: 0.6433 (t) REVERT: I 108 LEU cc_start: 0.9342 (tp) cc_final: 0.9055 (tp) REVERT: K 5 THR cc_start: 0.7648 (m) cc_final: 0.6991 (p) REVERT: K 42 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8277 (tp-100) REVERT: K 65 SER cc_start: 0.9341 (t) cc_final: 0.9063 (t) outliers start: 2 outliers final: 0 residues processed: 482 average time/residue: 0.1430 time to fit residues: 109.2727 Evaluate side-chains 385 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN I 95 GLN K 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093303 restraints weight = 43692.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096249 restraints weight = 27857.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098248 restraints weight = 21012.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099607 restraints weight = 17542.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100518 restraints weight = 15542.395| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21156 Z= 0.139 Angle : 0.680 15.250 28956 Z= 0.343 Chirality : 0.047 0.535 3582 Planarity : 0.004 0.064 3417 Dihedral : 4.846 36.256 2508 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.15 % Allowed : 0.39 % Favored : 99.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.03 (0.18), residues: 2307 helix: 0.92 (0.25), residues: 435 sheet: 0.48 (0.19), residues: 768 loop : -0.63 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 103 TYR 0.013 0.001 TYR A 217 PHE 0.020 0.002 PHE G 58 TRP 0.020 0.002 TRP I 36 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (20979) covalent geometry : angle 0.64404 / 0.34 (28458) SS BOND : bond 0.00322 / 0.21 ( 33) SS BOND : angle 1.19449 / 0.72 ( 66) hydrogen bonds : bond 0.04343 / 2.94 ( 735) hydrogen bonds : angle 5.22444 / 3.66 ( 1926) link_ALPHA1-2 : bond 0.00821 / 0.41 ( 3) link_ALPHA1-2 : angle 1.93954 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00576 / 0.28 ( 6) link_ALPHA1-3 : angle 1.30277 / 0.64 ( 18) link_ALPHA1-6 : bond 0.00560 / 0.31 ( 6) link_ALPHA1-6 : angle 1.32685 / 0.66 ( 18) link_BETA1-4 : bond 0.00521 / 0.27 ( 48) link_BETA1-4 : angle 1.41759 / 1.03 ( 144) link_NAG-ASN : bond 0.00340 / 0.23 ( 81) link_NAG-ASN : angle 2.14281 / 1.44 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 489 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8241 (m-30) cc_final: 0.7550 (p0) REVERT: A 217 TYR cc_start: 0.7606 (m-10) cc_final: 0.6515 (m-10) REVERT: A 425 ASN cc_start: 0.7766 (t0) cc_final: 0.7507 (t0) REVERT: B 543 GLN cc_start: 0.8127 (mt0) cc_final: 0.7888 (mt0) REVERT: B 584 GLU cc_start: 0.8870 (tt0) cc_final: 0.8356 (tp30) REVERT: B 634 GLU cc_start: 0.8647 (tt0) cc_final: 0.8236 (tt0) REVERT: H 47 TRP cc_start: 0.9016 (t60) cc_final: 0.8452 (t60) REVERT: H 50 TRP cc_start: 0.9342 (p-90) cc_final: 0.8594 (p-90) REVERT: H 89 THR cc_start: 0.9263 (m) cc_final: 0.8773 (p) REVERT: H 99 THR cc_start: 0.6356 (t) cc_final: 0.5320 (t) REVERT: H 100 TYR cc_start: 0.4858 (m-80) cc_final: 0.4433 (m-80) REVERT: H 108 LEU cc_start: 0.9365 (tp) cc_final: 0.9079 (tp) REVERT: L 42 GLN cc_start: 0.8268 (tp40) cc_final: 0.7942 (tp-100) REVERT: L 46 LEU cc_start: 0.8287 (pt) cc_final: 0.7959 (pp) REVERT: L 60 ASP cc_start: 0.7826 (m-30) cc_final: 0.7442 (m-30) REVERT: L 66 GLN cc_start: 0.8277 (pt0) cc_final: 0.7952 (pt0) REVERT: L 70 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7472 (pp30) REVERT: L 96 GLU cc_start: 0.8350 (pt0) cc_final: 0.7277 (pt0) REVERT: C 180 ASP cc_start: 0.8457 (m-30) cc_final: 0.8253 (m-30) REVERT: C 217 TYR cc_start: 0.7785 (m-80) cc_final: 0.7317 (m-80) REVERT: C 354 ARG cc_start: 0.8041 (tpm170) cc_final: 0.7544 (tpm170) REVERT: C 373 MET cc_start: 0.8826 (mtm) cc_final: 0.8618 (mtm) REVERT: E 540 GLN cc_start: 0.8599 (mm110) cc_final: 0.7992 (mm-40) REVERT: E 584 GLU cc_start: 0.8716 (tt0) cc_final: 0.8427 (tp30) REVERT: E 601 LYS cc_start: 0.8833 (mttt) cc_final: 0.8564 (mtmm) REVERT: E 648 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7612 (tm-30) REVERT: D 53 PHE cc_start: 0.8388 (p90) cc_final: 0.8021 (p90) REVERT: D 95 MET cc_start: 0.7821 (ptm) cc_final: 0.6823 (ppp) REVERT: D 203 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 466 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7947 (mp0) REVERT: F 621 ASN cc_start: 0.8060 (t0) cc_final: 0.7738 (t0) REVERT: F 643 TYR cc_start: 0.8883 (m-80) cc_final: 0.8483 (m-80) REVERT: G 36 TRP cc_start: 0.9168 (m100) cc_final: 0.8105 (m100) REVERT: G 39 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8117 (tm-30) REVERT: G 47 TRP cc_start: 0.8809 (t60) cc_final: 0.8297 (t60) REVERT: G 50 TRP cc_start: 0.9265 (p-90) cc_final: 0.8853 (p-90) REVERT: G 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7984 (t0) REVERT: G 89 THR cc_start: 0.9097 (m) cc_final: 0.8601 (p) REVERT: G 95 GLN cc_start: 0.7866 (tt0) cc_final: 0.7564 (tm-30) REVERT: G 99 THR cc_start: 0.6204 (t) cc_final: 0.5882 (t) REVERT: G 108 LEU cc_start: 0.8879 (tp) cc_final: 0.8667 (tp) REVERT: J 34 THR cc_start: 0.8993 (m) cc_final: 0.8448 (p) REVERT: J 42 GLN cc_start: 0.8087 (tp40) cc_final: 0.7785 (tp-100) REVERT: J 96 GLU cc_start: 0.8617 (pt0) cc_final: 0.8038 (pt0) REVERT: I 21 SER cc_start: 0.8688 (p) cc_final: 0.8438 (p) REVERT: I 65 GLN cc_start: 0.8577 (tt0) cc_final: 0.8321 (mt0) REVERT: I 89 THR cc_start: 0.9033 (m) cc_final: 0.8589 (p) REVERT: I 99 THR cc_start: 0.6466 (t) cc_final: 0.5827 (t) REVERT: I 108 LEU cc_start: 0.9315 (tp) cc_final: 0.9019 (tp) REVERT: K 5 THR cc_start: 0.7652 (m) cc_final: 0.6981 (p) REVERT: K 33 MET cc_start: 0.6286 (pmm) cc_final: 0.5622 (pmm) REVERT: K 42 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8187 (tp-100) REVERT: K 65 SER cc_start: 0.9340 (t) cc_final: 0.9130 (t) REVERT: K 86 TYR cc_start: 0.7946 (m-10) cc_final: 0.7745 (m-10) outliers start: 3 outliers final: 0 residues processed: 489 average time/residue: 0.1434 time to fit residues: 111.0151 Evaluate side-chains 402 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 215 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 653 GLN L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN J 32 HIS J 70 GLN K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094768 restraints weight = 43869.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097572 restraints weight = 29080.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099487 restraints weight = 22388.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100763 restraints weight = 18895.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101533 restraints weight = 16861.766| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21156 Z= 0.131 Angle : 0.671 14.376 28956 Z= 0.339 Chirality : 0.047 0.500 3582 Planarity : 0.005 0.062 3417 Dihedral : 4.773 36.327 2508 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.02 (0.17), residues: 2307 helix: 0.98 (0.25), residues: 432 sheet: 0.45 (0.19), residues: 774 loop : -0.64 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 31 TYR 0.014 0.001 TYR A 217 PHE 0.031 0.002 PHE I 58 TRP 0.032 0.002 TRP H 36 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20979) covalent geometry : angle 0.63877 / 0.33 (28458) SS BOND : bond 0.00304 / 0.19 ( 33) SS BOND : angle 1.13494 / 0.69 ( 66) hydrogen bonds : bond 0.04217 / 2.86 ( 735) hydrogen bonds : angle 5.22198 / 3.64 ( 1926) link_ALPHA1-2 : bond 0.00834 / 0.42 ( 3) link_ALPHA1-2 : angle 1.90300 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00544 / 0.28 ( 6) link_ALPHA1-3 : angle 1.30346 / 0.64 ( 18) link_ALPHA1-6 : bond 0.00511 / 0.28 ( 6) link_ALPHA1-6 : angle 1.36717 / 0.68 ( 18) link_BETA1-4 : bond 0.00520 / 0.28 ( 48) link_BETA1-4 : angle 1.38352 / 1.00 ( 144) link_NAG-ASN : bond 0.00340 / 0.22 ( 81) link_NAG-ASN : angle 2.01596 / 1.35 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 494 time to evaluate : 0.770 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 78 ASP cc_start: 0.8259 (m-30) cc_final: 0.7583 (p0) REVERT: A 217 TYR cc_start: 0.7260 (m-10) cc_final: 0.6517 (m-10) REVERT: A 425 ASN cc_start: 0.7771 (t0) cc_final: 0.7480 (t0) REVERT: A 453 LEU cc_start: 0.9132 (mt) cc_final: 0.8778 (mp) REVERT: B 543 GLN cc_start: 0.8058 (mt0) cc_final: 0.7833 (mt0) REVERT: B 584 GLU cc_start: 0.8836 (tt0) cc_final: 0.8323 (tp30) REVERT: B 634 GLU cc_start: 0.8454 (tt0) cc_final: 0.8117 (tt0) REVERT: H 47 TRP cc_start: 0.9005 (t60) cc_final: 0.8419 (t60) REVERT: H 50 TRP cc_start: 0.9164 (p-90) cc_final: 0.8580 (p-90) REVERT: H 89 THR cc_start: 0.9221 (m) cc_final: 0.8752 (p) REVERT: H 99 THR cc_start: 0.6423 (t) cc_final: 0.5540 (t) REVERT: H 100 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6369 (tm-30) REVERT: H 100 TYR cc_start: 0.4830 (m-80) cc_final: 0.4454 (m-80) REVERT: H 108 LEU cc_start: 0.9355 (tp) cc_final: 0.9069 (tp) REVERT: L 42 GLN cc_start: 0.8171 (tp40) cc_final: 0.7851 (tp-100) REVERT: L 60 ASP cc_start: 0.7912 (m-30) cc_final: 0.7557 (m-30) REVERT: L 66 GLN cc_start: 0.8253 (pt0) cc_final: 0.8050 (pt0) REVERT: L 70 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: L 96 GLU cc_start: 0.8226 (pt0) cc_final: 0.7036 (pt0) REVERT: C 205 CYS cc_start: 0.7820 (m) cc_final: 0.7574 (m) REVERT: C 217 TYR cc_start: 0.7661 (m-80) cc_final: 0.7255 (m-80) REVERT: C 348 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8386 (mmtm) REVERT: C 354 ARG cc_start: 0.7934 (tpm170) cc_final: 0.7453 (tpm170) REVERT: E 537 LEU cc_start: 0.8162 (mt) cc_final: 0.7942 (mt) REVERT: E 540 GLN cc_start: 0.8605 (mm110) cc_final: 0.8029 (mm-40) REVERT: E 584 GLU cc_start: 0.8599 (tt0) cc_final: 0.8381 (tp30) REVERT: E 601 LYS cc_start: 0.8840 (mttt) cc_final: 0.8553 (mtmm) REVERT: E 648 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7592 (tm-30) REVERT: D 53 PHE cc_start: 0.8424 (p90) cc_final: 0.8048 (p90) REVERT: D 69 TRP cc_start: 0.5774 (p-90) cc_final: 0.5381 (p-90) REVERT: D 95 MET cc_start: 0.7748 (ptm) cc_final: 0.7018 (ppp) REVERT: D 203 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8411 (tm-30) REVERT: D 466 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7801 (mp0) REVERT: F 621 ASN cc_start: 0.7979 (t0) cc_final: 0.7650 (t0) REVERT: G 36 TRP cc_start: 0.9077 (m100) cc_final: 0.8268 (m100) REVERT: G 39 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8120 (tm-30) REVERT: G 47 TRP cc_start: 0.8832 (t60) cc_final: 0.8357 (t60) REVERT: G 50 TRP cc_start: 0.9212 (p-90) cc_final: 0.8789 (p-90) REVERT: G 72 ASP cc_start: 0.8409 (t0) cc_final: 0.8021 (t0) REVERT: G 89 THR cc_start: 0.9029 (m) cc_final: 0.8566 (p) REVERT: G 95 GLN cc_start: 0.8051 (tt0) cc_final: 0.7777 (tm-30) REVERT: G 99 THR cc_start: 0.6126 (t) cc_final: 0.5618 (t) REVERT: G 108 LEU cc_start: 0.8827 (tp) cc_final: 0.8613 (tp) REVERT: J 34 THR cc_start: 0.8926 (m) cc_final: 0.8388 (p) REVERT: J 42 GLN cc_start: 0.8281 (tp40) cc_final: 0.7868 (tp-100) REVERT: J 66 GLN cc_start: 0.8273 (pp30) cc_final: 0.6931 (tp-100) REVERT: J 96 GLU cc_start: 0.8517 (pt0) cc_final: 0.7840 (pt0) REVERT: I 21 SER cc_start: 0.8680 (p) cc_final: 0.8403 (p) REVERT: I 65 GLN cc_start: 0.8538 (tt0) cc_final: 0.8327 (mt0) REVERT: I 89 THR cc_start: 0.9045 (m) cc_final: 0.8620 (p) REVERT: I 99 THR cc_start: 0.6714 (t) cc_final: 0.5947 (t) REVERT: I 108 LEU cc_start: 0.9310 (tp) cc_final: 0.9031 (tp) REVERT: K 5 THR cc_start: 0.7594 (m) cc_final: 0.6943 (p) REVERT: K 33 MET cc_start: 0.6221 (pmm) cc_final: 0.5619 (pmm) REVERT: K 65 SER cc_start: 0.9308 (t) cc_final: 0.9064 (t) REVERT: K 86 TYR cc_start: 0.7908 (m-10) cc_final: 0.7706 (m-10) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.1439 time to fit residues: 112.7332 Evaluate side-chains 401 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 146 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN F 652 GLN J 70 GLN K 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094470 restraints weight = 43674.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097459 restraints weight = 27699.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099480 restraints weight = 20836.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100724 restraints weight = 17352.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101701 restraints weight = 15449.500| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21156 Z= 0.131 Angle : 0.663 13.839 28956 Z= 0.335 Chirality : 0.047 0.472 3582 Planarity : 0.005 0.062 3417 Dihedral : 4.691 35.488 2508 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.03 (0.17), residues: 2307 helix: 1.01 (0.25), residues: 432 sheet: 0.48 (0.19), residues: 768 loop : -0.67 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 103 TYR 0.018 0.001 TYR A 217 PHE 0.034 0.002 PHE I 58 TRP 0.041 0.002 TRP H 36 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20979) covalent geometry : angle 0.63147 / 0.33 (28458) SS BOND : bond 0.00289 / 0.19 ( 33) SS BOND : angle 1.13981 / 0.72 ( 66) hydrogen bonds : bond 0.04156 / 2.82 ( 735) hydrogen bonds : angle 5.16593 / 3.60 ( 1926) link_ALPHA1-2 : bond 0.00827 / 0.41 ( 3) link_ALPHA1-2 : angle 1.88582 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00518 / 0.27 ( 6) link_ALPHA1-3 : angle 1.28359 / 0.63 ( 18) link_ALPHA1-6 : bond 0.00524 / 0.29 ( 6) link_ALPHA1-6 : angle 1.35321 / 0.67 ( 18) link_BETA1-4 : bond 0.00493 / 0.26 ( 48) link_BETA1-4 : angle 1.36384 / 0.99 ( 144) link_NAG-ASN : bond 0.00326 / 0.22 ( 81) link_NAG-ASN : angle 1.95373 / 1.30 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.19 seconds wall clock time: 68 minutes 38.90 seconds (4118.90 seconds total)