Starting phenix.real_space_refine on Sun Jul 5 03:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ucg_26443/07_2026/7ucg_26443.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 141 5.16 5 C 15924 2.51 5 N 4266 2.21 5 O 5058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 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: 25389 Number of models: 1 Model: "" Number of chains: 48 Chain: "B" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 727 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3455 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 3 Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 727 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3455 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 3 Chain: "J" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "N" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 727 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3455 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 3 Chain: "Q" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} 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: 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: "X" 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: "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: 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: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "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: 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: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 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: 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.00, per 1000 atoms: 0.24 Number of scatterers: 25389 At special positions: 0 Unit cell: (152.075, 159.027, 145.992, 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 141 16.00 O 5058 8.00 N 4266 7.00 C 15924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 376 " - pdb=" SG CYS G 443 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 416 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS I 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 376 " - pdb=" SG CYS I 443 " distance=2.03 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 416 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 605 " - pdb=" SG CYS P 498 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.04 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 376 " - pdb=" SG CYS P 443 " distance=2.03 Simple disulfide: pdb=" SG CYS P 383 " - pdb=" SG CYS P 416 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 91 " 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 b 4 " - " MAN b 5 " " MAN j 4 " - " MAN j 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " MAN b 6 " - " MAN b 7 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " " MAN r 6 " - " MAN r 7 " ALPHA1-6 " BMA X 3 " - " MAN X 5 " " BMA b 3 " - " MAN b 6 " " BMA f 3 " - " MAN f 5 " " BMA j 3 " - " MAN j 6 " " BMA n 3 " - " MAN n 5 " " BMA r 3 " - " MAN r 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 339 " " NAG G 606 " - " ASN G 390 " " NAG G 607 " - " ASN G 446 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 603 " - " ASN I 197 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG I 606 " - " ASN I 390 " " NAG I 607 " - " ASN I 446 " " NAG P 601 " - " ASN P 88 " " NAG P 602 " - " ASN P 160 " " NAG P 603 " - " ASN P 197 " " NAG P 604 " - " ASN P 339 " " NAG P 605 " - " ASN P 390 " " NAG P 606 " - " ASN P 446 " " NAG P 607 " - " ASN P 234 " " NAG S 1 " - " ASN E 19 " " NAG T 1 " - " ASN F 19 " " NAG U 1 " - " ASN O 19 " " NAG V 1 " - " ASN G 156 " " NAG W 1 " - " ASN G 241 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 276 " " NAG Z 1 " - " ASN G 295 " " NAG a 1 " - " ASN G 301 " " NAG b 1 " - " ASN G 332 " " NAG c 1 " - " ASN G 384 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 241 " " NAG f 1 " - " ASN I 262 " " NAG g 1 " - " ASN I 276 " " NAG h 1 " - " ASN I 295 " " NAG i 1 " - " ASN I 301 " " NAG j 1 " - " ASN I 332 " " NAG k 1 " - " ASN I 384 " " NAG l 1 " - " ASN P 156 " " NAG m 1 " - " ASN P 241 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 276 " " NAG p 1 " - " ASN P 295 " " NAG q 1 " - " ASN P 301 " " NAG r 1 " - " ASN P 332 " " NAG s 1 " - " ASN P 384 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5646 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 69 sheets defined 15.1% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.442A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.556A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.679A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.508A pdb=" N GLU B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.900A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 79 removed outlier: 3.504A pdb=" N ASP E 78 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU E 79 " --> pdb=" O THR E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 79' Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.516A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 352 removed outlier: 3.513A pdb=" N ILE G 343 " --> pdb=" O ASN G 339 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 371 Processing helix chain 'G' and resid 423 through 427 removed outlier: 3.736A pdb=" N GLN G 426 " --> pdb=" O ASN G 423 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU G 427 " --> pdb=" O MET G 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 423 through 427' Processing helix chain 'G' and resid 472 through 478 removed outlier: 3.634A pdb=" N TRP G 476 " --> pdb=" O MET G 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.518A pdb=" N ASP L 85 " --> pdb=" O GLU L 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.376A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.653A pdb=" N ARG A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.899A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.509A pdb=" N ASP F 78 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 79 " --> pdb=" O THR F 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 75 through 79' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.517A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.518A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 352 removed outlier: 3.560A pdb=" N ILE I 343 " --> pdb=" O ASN I 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 348 " --> pdb=" O GLN I 344 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 371 Processing helix chain 'I' and resid 423 through 427 removed outlier: 3.694A pdb=" N GLN I 426 " --> pdb=" O ASN I 423 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU I 427 " --> pdb=" O MET I 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 423 through 427' Processing helix chain 'I' and resid 472 through 478 removed outlier: 3.614A pdb=" N TRP I 476 " --> pdb=" O MET I 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'K' and resid 82 through 86 removed outlier: 3.733A pdb=" N GLU K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 534 Processing helix chain 'M' and resid 536 through 543 removed outlier: 4.359A pdb=" N GLN M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN M 543 " --> pdb=" O VAL M 539 " (cutoff:3.500A) Processing helix chain 'M' and resid 570 through 596 Processing helix chain 'M' and resid 619 through 624 removed outlier: 4.060A pdb=" N ASP M 624 " --> pdb=" O GLY M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 627 through 636 removed outlier: 3.633A pdb=" N TRP M 631 " --> pdb=" O THR M 627 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU M 634 " --> pdb=" O GLN M 630 " (cutoff:3.500A) Processing helix chain 'M' and resid 638 through 649 removed outlier: 3.537A pdb=" N GLU M 647 " --> pdb=" O PHE M 643 " (cutoff:3.500A) Processing helix chain 'M' and resid 650 through 662 removed outlier: 3.902A pdb=" N ASN M 656 " --> pdb=" O GLN M 652 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 removed outlier: 3.512A pdb=" N ASP O 78 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU O 79 " --> pdb=" O THR O 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 75 through 79' Processing helix chain 'P' and resid 99 through 116 removed outlier: 3.548A pdb=" N LEU P 116 " --> pdb=" O TRP P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.629A pdb=" N CYS P 126 " --> pdb=" O THR P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 352 removed outlier: 3.865A pdb=" N HIS P 352 " --> pdb=" O LYS P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 371 Processing helix chain 'P' and resid 423 through 427 removed outlier: 3.736A pdb=" N GLN P 426 " --> pdb=" O ASN P 423 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU P 427 " --> pdb=" O MET P 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 423 through 427' Processing helix chain 'P' and resid 472 through 478 removed outlier: 3.670A pdb=" N TRP P 476 " --> pdb=" O MET P 472 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER P 478 " --> pdb=" O ASP P 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 4.049A pdb=" N ASN Q 31 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR Q 32 " --> pdb=" O MET Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'R' and resid 82 through 86 removed outlier: 3.516A pdb=" N ASP R 85 " --> pdb=" O GLU R 82 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 82 through 86' Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.741A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.991A pdb=" N GLU D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 50 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.991A pdb=" N GLU D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 112 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.956A pdb=" N VAL E 10 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP E 31 " --> pdb=" O ILE E 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.956A pdb=" N VAL E 10 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.628A pdb=" N SER E 59 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 45 through 46 removed outlier: 4.092A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.191A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'G' and resid 130 through 133 removed outlier: 3.585A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 181 through 182 removed outlier: 3.576A pdb=" N ILE G 192 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.623A pdb=" N GLY G 449 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.623A pdb=" N GLY G 449 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 463 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 413 through 416 removed outlier: 3.713A pdb=" N ALA G 329 " --> pdb=" O CYS G 416 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS G 296 " --> pdb=" O CYS G 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'G' and resid 372 through 375 removed outlier: 3.581A pdb=" N PHE G 374 " --> pdb=" O PHE G 381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.999A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 80 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP H 72 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.869A pdb=" N THR H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR H 50 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 96 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE H 114 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.869A pdb=" N THR H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR H 50 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 96 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.459A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN L 37 " --> pdb=" O ILE L 45 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AC6, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.727A pdb=" N CYS A 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL I 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL I 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.523A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.980A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.980A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 112 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.734A pdb=" N SER F 59 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 40 through 45 removed outlier: 7.002A pdb=" N TRP F 31 " --> pdb=" O ILE F 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 40 through 45 removed outlier: 7.002A pdb=" N TRP F 31 " --> pdb=" O ILE F 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 46 removed outlier: 4.129A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.126A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 91 through 93 removed outlier: 3.528A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'I' and resid 259 through 260 Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 260 removed outlier: 3.653A pdb=" N GLY I 463 " --> pdb=" O THR I 356 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE I 465 " --> pdb=" O LYS I 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 294 through 296 removed outlier: 3.757A pdb=" N ALA I 329 " --> pdb=" O CYS I 416 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE I 380 " --> pdb=" O LYS I 419 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE I 374 " --> pdb=" O PHE I 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 301 through 308 removed outlier: 7.537A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.886A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP J 72 " --> pdb=" O GLN J 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 58 removed outlier: 3.877A pdb=" N THR J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR J 50 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 96 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE J 114 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 57 through 58 removed outlier: 3.877A pdb=" N THR J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR J 50 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 96 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 67 through 68 Processing sheet with id=AE9, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.633A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF2, first strand: chain 'M' and resid 603 through 609 removed outlier: 3.699A pdb=" N CYS M 604 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL P 38 " --> pdb=" O CYS M 604 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR M 606 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL P 36 " --> pdb=" O THR M 606 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.522A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AF5, first strand: chain 'N' and resid 59 through 60 removed outlier: 3.504A pdb=" N TRP N 50 " --> pdb=" O ASN N 59 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE N 112 " --> pdb=" O THR N 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 59 through 60 removed outlier: 3.504A pdb=" N TRP N 50 " --> pdb=" O ASN N 59 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 9 through 10 removed outlier: 3.984A pdb=" N VAL O 10 " --> pdb=" O LYS O 95 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TRP O 31 " --> pdb=" O ILE O 43 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 9 through 10 removed outlier: 3.984A pdb=" N VAL O 10 " --> pdb=" O LYS O 95 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.699A pdb=" N SER O 59 " --> pdb=" O THR O 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.927A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 75 through 76 removed outlier: 4.160A pdb=" N VAL P 75 " --> pdb=" O CYS P 54 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.637A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 130 through 133 Processing sheet with id=AG5, first strand: chain 'P' and resid 181 through 182 Processing sheet with id=AG6, first strand: chain 'P' and resid 259 through 260 removed outlier: 3.522A pdb=" N GLY P 449 " --> pdb=" O LEU P 260 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 259 through 260 removed outlier: 3.522A pdb=" N GLY P 449 " --> pdb=" O LEU P 260 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 372 through 376 removed outlier: 3.547A pdb=" N PHE P 374 " --> pdb=" O PHE P 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE P 380 " --> pdb=" O LYS P 419 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA P 329 " --> pdb=" O CYS P 416 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS P 296 " --> pdb=" O CYS P 443 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 304 through 308 Processing sheet with id=AH1, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.824A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP Q 72 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 57 through 58 removed outlier: 3.847A pdb=" N THR Q 58 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 96 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE Q 114 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 57 through 58 removed outlier: 3.847A pdb=" N THR Q 58 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 96 " --> pdb=" O THR Q 35 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 67 through 68 Processing sheet with id=AH5, first strand: chain 'R' and resid 9 through 11 removed outlier: 6.579A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 19 through 22 768 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7997 1.35 - 1.47: 6680 1.47 - 1.60: 11057 1.60 - 1.72: 0 1.72 - 1.85: 192 Bond restraints: 25926 Sorted by residual: bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.560 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" N ILE P 357 " pdb=" CA ILE P 357 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.26e+00 ... (remaining 25921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 34833 3.86 - 7.72: 340 7.72 - 11.59: 28 11.59 - 15.45: 5 15.45 - 19.31: 2 Bond angle restraints: 35208 Sorted by residual: angle pdb=" C ASN I 234 " pdb=" CA ASN I 234 " pdb=" CB ASN I 234 " ideal model delta sigma weight residual 110.92 99.65 11.27 1.59e+00 3.96e-01 5.03e+01 angle pdb=" C SER M 553 " pdb=" N ASN M 554 " pdb=" CA ASN M 554 " ideal model delta sigma weight residual 121.70 132.55 -10.85 1.80e+00 3.09e-01 3.63e+01 angle pdb=" C SER B 553 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " ideal model delta sigma weight residual 121.70 132.27 -10.57 1.80e+00 3.09e-01 3.45e+01 angle pdb=" C SER A 553 " pdb=" N ASN A 554 " pdb=" CA ASN A 554 " ideal model delta sigma weight residual 121.70 131.99 -10.29 1.80e+00 3.09e-01 3.27e+01 angle pdb=" CA LEU A 555 " pdb=" CB LEU A 555 " pdb=" CG LEU A 555 " ideal model delta sigma weight residual 116.30 135.61 -19.31 3.50e+00 8.16e-02 3.04e+01 ... (remaining 35203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13257 17.88 - 35.75: 1159 35.75 - 53.63: 213 53.63 - 71.51: 51 71.51 - 89.38: 26 Dihedral angle restraints: 14706 sinusoidal: 5901 harmonic: 8805 Sorted by residual: dihedral pdb=" CA ASN I 234 " pdb=" C ASN I 234 " pdb=" N GLY I 235 " pdb=" CA GLY I 235 " ideal model delta harmonic sigma weight residual -180.00 -131.46 -48.54 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" CA SER I 334 " pdb=" C SER I 334 " pdb=" N ARG I 335 " pdb=" CA ARG I 335 " ideal model delta harmonic sigma weight residual 180.00 144.56 35.44 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA SER G 334 " pdb=" C SER G 334 " pdb=" N ARG G 335 " pdb=" CA ARG G 335 " ideal model delta harmonic sigma weight residual 180.00 145.19 34.81 0 5.00e+00 4.00e-02 4.85e+01 ... (remaining 14703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 4165 0.267 - 0.534: 14 0.534 - 0.800: 3 0.800 - 1.067: 1 1.067 - 1.334: 2 Chirality restraints: 4185 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN I 156 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.07 -1.33 2.00e-01 2.50e+01 4.45e+01 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN I 276 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" C1 NAG I 604 " pdb=" ND2 ASN I 234 " pdb=" C2 NAG I 604 " pdb=" O5 NAG I 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 4182 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 607 " 0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG P 607 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG P 607 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG P 607 " -0.168 2.00e-02 2.50e+03 pdb=" O7 NAG P 607 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 234 " 0.008 2.00e-02 2.50e+03 5.52e-02 3.81e+01 pdb=" CG ASN I 234 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN I 234 " 0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN I 234 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG I 604 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS O 35 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO O 36 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO O 36 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO O 36 " -0.056 5.00e-02 4.00e+02 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4905 2.78 - 3.31: 22246 3.31 - 3.84: 41274 3.84 - 4.37: 46941 4.37 - 4.90: 82612 Nonbonded interactions: 197978 Sorted by model distance: nonbonded pdb=" O GLN A 575 " pdb=" OG1 THR A 578 " model vdw 2.253 3.040 nonbonded pdb=" O GLN M 575 " pdb=" OG1 THR M 578 " model vdw 2.265 3.040 nonbonded pdb=" NH2 ARG A 585 " pdb=" O ILE I 488 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP N 103 " pdb=" OH TYR O 45 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASN L 50 " pdb=" O6 MAN b 5 " model vdw 2.302 3.040 ... (remaining 197973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'X' selection = chain 'f' selection = chain 'n' } ncs_group { reference = chain 'b' selection = chain 'j' selection = chain 'r' } 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: 4.430 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.710 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 26067 Z= 0.279 Angle : 1.050 25.104 35589 Z= 0.516 Chirality : 0.067 1.334 4185 Planarity : 0.006 0.106 4353 Dihedral : 14.199 89.382 8934 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.36 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.34 (0.14), residues: 3003 helix: -2.07 (0.23), residues: 333 sheet: -1.14 (0.17), residues: 867 loop : -1.69 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 308 TYR 0.033 0.001 TYR M 638 PHE 0.013 0.002 PHE I 233 TRP 0.063 0.002 TRP M 610 HIS 0.005 0.001 HIS I 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 (25926) covalent geometry : angle 0.97645 / 0.50 (35208) SS BOND : bond 0.00489 / 0.31 ( 42) SS BOND : angle 1.23430 / 0.80 ( 84) hydrogen bonds : bond 0.28168 / 18.86 ( 705) hydrogen bonds : angle 10.66897 / 7.65 ( 1941) link_ALPHA1-2 : bond 0.00316 / 0.18 ( 3) link_ALPHA1-2 : angle 1.70710 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00419 / 0.28 ( 9) link_ALPHA1-3 : angle 2.28833 / 1.34 ( 27) link_ALPHA1-6 : bond 0.00333 / 0.20 ( 6) link_ALPHA1-6 : angle 1.70237 / 1.14 ( 18) link_BETA1-4 : bond 0.01033 / 0.69 ( 33) link_BETA1-4 : angle 2.82197 / 1.96 ( 99) link_NAG-ASN : bond 0.00997 / 0.69 ( 48) link_NAG-ASN : angle 5.61265 / 3.86 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.988 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: B 535 MET cc_start: 0.6330 (ttp) cc_final: 0.5423 (mtt) REVERT: B 542 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6986 (mtm-85) REVERT: B 617 LYS cc_start: 0.8508 (mttm) cc_final: 0.8196 (mttm) REVERT: H 29 MET cc_start: 0.3142 (mmp) cc_final: 0.2037 (ppp) REVERT: A 617 LYS cc_start: 0.8348 (mttp) cc_final: 0.8143 (mtpm) REVERT: A 641 THR cc_start: 0.7771 (t) cc_final: 0.7320 (m) REVERT: F 49 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6997 (mtp180) REVERT: I 164 GLU cc_start: 0.6441 (mp0) cc_final: 0.6189 (mp0) REVERT: I 274 SER cc_start: 0.8012 (t) cc_final: 0.7802 (t) REVERT: M 535 MET cc_start: 0.6810 (ttm) cc_final: 0.5857 (mtt) REVERT: Q 105 TYR cc_start: 0.8370 (p90) cc_final: 0.8118 (p90) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.1806 time to fit residues: 158.8957 Evaluate side-chains 417 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN C 39 GLN I 170 GLN J 102 GLN M 630 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.208155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.171644 restraints weight = 34728.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171794 restraints weight = 33091.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173160 restraints weight = 29106.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173937 restraints weight = 21841.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174933 restraints weight = 20658.545| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26067 Z= 0.134 Angle : 0.712 20.496 35589 Z= 0.342 Chirality : 0.049 0.820 4185 Planarity : 0.005 0.066 4353 Dihedral : 5.040 38.197 3312 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.20 % Favored : 95.47 % Rotamer: Outliers : 1.66 % Allowed : 9.68 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.14), residues: 3003 helix: -0.62 (0.25), residues: 369 sheet: -0.85 (0.16), residues: 933 loop : -1.70 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 417 TYR 0.016 0.001 TYR M 638 PHE 0.010 0.001 PHE J 114 TRP 0.021 0.002 TRP B 610 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (25926) covalent geometry : angle 0.65887 / 0.33 (35208) SS BOND : bond 0.00308 / 0.20 ( 42) SS BOND : angle 0.79808 / 0.52 ( 84) hydrogen bonds : bond 0.04958 / 3.35 ( 705) hydrogen bonds : angle 7.00217 / 5.01 ( 1941) link_ALPHA1-2 : bond 0.00479 / 0.27 ( 3) link_ALPHA1-2 : angle 1.40862 / 0.92 ( 9) link_ALPHA1-3 : bond 0.00506 / 0.34 ( 9) link_ALPHA1-3 : angle 1.93459 / 1.15 ( 27) link_ALPHA1-6 : bond 0.00443 / 0.29 ( 6) link_ALPHA1-6 : angle 1.38701 / 0.94 ( 18) link_BETA1-4 : bond 0.00533 / 0.37 ( 33) link_BETA1-4 : angle 1.78461 / 1.28 ( 99) link_NAG-ASN : bond 0.00842 / 0.60 ( 48) link_NAG-ASN : angle 3.94250 / 2.68 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 431 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.6448 (ttp) cc_final: 0.5632 (mtt) REVERT: B 573 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6653 (tp) REVERT: B 617 LYS cc_start: 0.8510 (mttm) cc_final: 0.8155 (mttm) REVERT: A 573 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 584 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 641 THR cc_start: 0.8015 (t) cc_final: 0.7607 (m) REVERT: A 651 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7741 (t0) REVERT: C 10 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6200 (mt-10) REVERT: C 28 ASN cc_start: 0.7751 (t0) cc_final: 0.7543 (t0) REVERT: C 39 GLN cc_start: 0.5670 (tt0) cc_final: 0.5442 (tt0) REVERT: F 49 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6901 (mtp180) REVERT: I 164 GLU cc_start: 0.6670 (mp0) cc_final: 0.6225 (mp0) REVERT: I 334 SER cc_start: 0.6649 (OUTLIER) cc_final: 0.6358 (m) REVERT: I 362 SER cc_start: 0.7953 (t) cc_final: 0.7734 (t) REVERT: J 99 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7119 (ptt180) REVERT: J 100 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.6925 (ttp80) REVERT: M 535 MET cc_start: 0.7053 (ttm) cc_final: 0.6013 (mtt) REVERT: M 573 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6972 (tp) REVERT: M 644 ARG cc_start: 0.7410 (mmt-90) cc_final: 0.7114 (mmt180) REVERT: Q 105 TYR cc_start: 0.8549 (p90) cc_final: 0.8274 (p90) outliers start: 44 outliers final: 28 residues processed: 454 average time/residue: 0.1894 time to fit residues: 128.8242 Evaluate side-chains 417 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 383 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 375 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 99 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 217 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 201 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN I 258 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.204844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168131 restraints weight = 34648.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167059 restraints weight = 34642.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169372 restraints weight = 32647.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169717 restraints weight = 21977.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170264 restraints weight = 20933.118| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26067 Z= 0.125 Angle : 0.661 18.902 35589 Z= 0.316 Chirality : 0.047 0.667 4185 Planarity : 0.004 0.052 4353 Dihedral : 4.759 32.543 3312 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.20 % Favored : 95.47 % Rotamer: Outliers : 2.00 % Allowed : 12.96 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 3003 helix: 0.15 (0.27), residues: 369 sheet: -0.65 (0.16), residues: 936 loop : -1.45 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 62 TYR 0.012 0.001 TYR R 49 PHE 0.023 0.001 PHE D 64 TRP 0.031 0.001 TRP B 610 HIS 0.005 0.001 HIS R 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25926) covalent geometry : angle 0.61294 / 0.31 (35208) SS BOND : bond 0.00398 / 0.25 ( 42) SS BOND : angle 0.85062 / 0.56 ( 84) hydrogen bonds : bond 0.04061 / 2.73 ( 705) hydrogen bonds : angle 6.12056 / 4.35 ( 1941) link_ALPHA1-2 : bond 0.00351 / 0.20 ( 3) link_ALPHA1-2 : angle 1.49775 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00519 / 0.35 ( 9) link_ALPHA1-3 : angle 1.85996 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00332 / 0.21 ( 6) link_ALPHA1-6 : angle 1.45023 / 0.98 ( 18) link_BETA1-4 : bond 0.00564 / 0.37 ( 33) link_BETA1-4 : angle 1.63927 / 1.14 ( 99) link_NAG-ASN : bond 0.00762 / 0.55 ( 48) link_NAG-ASN : angle 3.56053 / 2.40 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 408 time to evaluate : 0.963 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: B 535 MET cc_start: 0.6508 (ttp) cc_final: 0.5701 (mtt) REVERT: B 544 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7431 (mp) REVERT: B 617 LYS cc_start: 0.8541 (mttm) cc_final: 0.8114 (mttm) REVERT: L 93 MET cc_start: 0.7551 (ttt) cc_final: 0.7321 (ttt) REVERT: A 641 THR cc_start: 0.7984 (t) cc_final: 0.7556 (m) REVERT: A 651 ASN cc_start: 0.8101 (t0) cc_final: 0.7889 (t0) REVERT: F 49 ARG cc_start: 0.7418 (ttm170) cc_final: 0.6917 (mtp180) REVERT: I 164 GLU cc_start: 0.6531 (mp0) cc_final: 0.5855 (mp0) REVERT: J 99 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7169 (ptt180) REVERT: M 583 ILE cc_start: 0.8989 (mm) cc_final: 0.8736 (mt) REVERT: M 644 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7180 (mmt180) REVERT: P 432 MET cc_start: 0.8452 (ptm) cc_final: 0.8086 (ptp) outliers start: 53 outliers final: 26 residues processed: 434 average time/residue: 0.1879 time to fit residues: 122.7657 Evaluate side-chains 393 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 365 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain R residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 201 optimal weight: 2.9990 chunk 249 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 115 GLN E 34 GLN G 258 GLN G 344 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN I 344 GLN J 60 ASN K 50 ASN M 591 GLN O 34 GLN O 35 HIS ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 GLN R 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.193812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154468 restraints weight = 34399.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152979 restraints weight = 35190.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154941 restraints weight = 33954.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155489 restraints weight = 24336.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155720 restraints weight = 22766.714| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 26067 Z= 0.269 Angle : 0.802 19.532 35589 Z= 0.384 Chirality : 0.051 0.689 4185 Planarity : 0.005 0.049 4353 Dihedral : 5.123 29.964 3312 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.33 % Favored : 94.34 % Rotamer: Outliers : 2.90 % Allowed : 14.50 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3003 helix: -0.08 (0.26), residues: 375 sheet: -0.88 (0.17), residues: 984 loop : -1.45 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 542 TYR 0.019 0.002 TYR I 217 PHE 0.019 0.002 PHE C 29 TRP 0.038 0.002 TRP P 35 HIS 0.007 0.002 HIS P 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 (25926) covalent geometry : angle 0.75607 / 0.37 (35208) SS BOND : bond 0.00444 / 0.29 ( 42) SS BOND : angle 1.21992 / 0.81 ( 84) hydrogen bonds : bond 0.04372 / 2.93 ( 705) hydrogen bonds : angle 6.09125 / 4.31 ( 1941) link_ALPHA1-2 : bond 0.00026 / 0.01 ( 3) link_ALPHA1-2 : angle 1.93340 / 1.26 ( 9) link_ALPHA1-3 : bond 0.00294 / 0.19 ( 9) link_ALPHA1-3 : angle 1.86825 / 1.10 ( 27) link_ALPHA1-6 : bond 0.00159 / 0.11 ( 6) link_ALPHA1-6 : angle 1.42477 / 0.97 ( 18) link_BETA1-4 : bond 0.00593 / 0.39 ( 33) link_BETA1-4 : angle 2.06596 / 1.44 ( 99) link_NAG-ASN : bond 0.01081 / 0.71 ( 48) link_NAG-ASN : angle 3.77056 / 2.59 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 395 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 544 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 617 LYS cc_start: 0.8582 (mttm) cc_final: 0.8135 (mttm) REVERT: D 31 ASP cc_start: 0.8057 (m-30) cc_final: 0.7857 (m-30) REVERT: H 29 MET cc_start: 0.2575 (mmt) cc_final: 0.2268 (tmm) REVERT: A 647 GLU cc_start: 0.7946 (tt0) cc_final: 0.7708 (tt0) REVERT: C 28 ASN cc_start: 0.8026 (t0) cc_final: 0.7771 (t0) REVERT: F 49 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7342 (mtt90) REVERT: I 164 GLU cc_start: 0.6843 (mp0) cc_final: 0.6571 (mp0) REVERT: I 334 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6950 (m) REVERT: J 99 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7306 (ptt180) REVERT: M 583 ILE cc_start: 0.9146 (mm) cc_final: 0.8880 (mt) REVERT: P 199 SER cc_start: 0.8459 (p) cc_final: 0.8010 (m) REVERT: P 308 ARG cc_start: 0.7133 (mmp-170) cc_final: 0.6590 (mmm-85) outliers start: 77 outliers final: 54 residues processed: 445 average time/residue: 0.1826 time to fit residues: 121.9717 Evaluate side-chains 416 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 359 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 523 LEU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 357 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 392 THR Chi-restraints excluded: chain P residue 424 MET Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.0070 chunk 288 optimal weight: 0.0980 chunk 85 optimal weight: 0.0040 chunk 205 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 34 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN K 50 ASN K 52 GLN O 34 GLN ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.160593 restraints weight = 34112.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159119 restraints weight = 34758.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160962 restraints weight = 32543.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161628 restraints weight = 23220.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161780 restraints weight = 22212.408| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26067 Z= 0.111 Angle : 0.647 18.147 35589 Z= 0.307 Chirality : 0.046 0.623 4185 Planarity : 0.004 0.046 4353 Dihedral : 4.765 32.138 3312 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.06 % Favored : 95.60 % Rotamer: Outliers : 2.34 % Allowed : 16.76 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3003 helix: 0.41 (0.27), residues: 375 sheet: -0.84 (0.17), residues: 963 loop : -1.32 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 417 TYR 0.014 0.001 TYR P 433 PHE 0.013 0.001 PHE D 64 TRP 0.021 0.001 TRP Q 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (25926) covalent geometry : angle 0.60506 / 0.30 (35208) SS BOND : bond 0.00327 / 0.21 ( 42) SS BOND : angle 0.97370 / 0.65 ( 84) hydrogen bonds : bond 0.03465 / 2.32 ( 705) hydrogen bonds : angle 5.76340 / 4.08 ( 1941) link_ALPHA1-2 : bond 0.00302 / 0.16 ( 3) link_ALPHA1-2 : angle 1.54732 / 0.92 ( 9) link_ALPHA1-3 : bond 0.00421 / 0.29 ( 9) link_ALPHA1-3 : angle 1.83186 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00284 / 0.18 ( 6) link_ALPHA1-6 : angle 1.36908 / 0.93 ( 18) link_BETA1-4 : bond 0.00565 / 0.38 ( 33) link_BETA1-4 : angle 1.56890 / 1.09 ( 99) link_NAG-ASN : bond 0.00669 / 0.48 ( 48) link_NAG-ASN : angle 3.25503 / 2.21 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 379 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 544 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 617 LYS cc_start: 0.8546 (mttm) cc_final: 0.8251 (mttm) REVERT: G 164 GLU cc_start: 0.6683 (mp0) cc_final: 0.6187 (mp0) REVERT: A 544 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 663 LEU cc_start: 0.7453 (mt) cc_final: 0.7166 (mt) REVERT: I 164 GLU cc_start: 0.6769 (mp0) cc_final: 0.6494 (mp0) REVERT: J 99 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7310 (ptt180) REVERT: J 100 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7145 (ttp80) REVERT: M 583 ILE cc_start: 0.9004 (mm) cc_final: 0.8663 (mt) REVERT: N 62 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7294 (ttp-170) REVERT: P 51 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8857 (p) REVERT: P 164 GLU cc_start: 0.6698 (mp0) cc_final: 0.6191 (mp0) outliers start: 62 outliers final: 37 residues processed: 420 average time/residue: 0.1809 time to fit residues: 115.2525 Evaluate side-chains 392 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 351 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 259 LEU Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 3 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 266 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 221 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN A 630 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN R 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.193660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156227 restraints weight = 34320.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155231 restraints weight = 35749.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156917 restraints weight = 34162.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157390 restraints weight = 23686.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157685 restraints weight = 22789.011| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26067 Z= 0.228 Angle : 0.727 18.229 35589 Z= 0.347 Chirality : 0.049 0.620 4185 Planarity : 0.004 0.046 4353 Dihedral : 4.910 29.675 3312 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.26 % Favored : 94.41 % Rotamer: Outliers : 3.16 % Allowed : 16.72 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3003 helix: 0.27 (0.27), residues: 375 sheet: -0.85 (0.17), residues: 978 loop : -1.32 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.016 0.002 TYR H 32 PHE 0.016 0.002 PHE C 29 TRP 0.028 0.002 TRP H 34 HIS 0.005 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (25926) covalent geometry : angle 0.68532 / 0.34 (35208) SS BOND : bond 0.00445 / 0.29 ( 42) SS BOND : angle 1.05881 / 0.72 ( 84) hydrogen bonds : bond 0.03933 / 2.63 ( 705) hydrogen bonds : angle 5.75452 / 4.06 ( 1941) link_ALPHA1-2 : bond 0.00180 / 0.09 ( 3) link_ALPHA1-2 : angle 1.83152 / 1.19 ( 9) link_ALPHA1-3 : bond 0.00323 / 0.21 ( 9) link_ALPHA1-3 : angle 1.88730 / 1.12 ( 27) link_ALPHA1-6 : bond 0.00197 / 0.13 ( 6) link_ALPHA1-6 : angle 1.39069 / 0.94 ( 18) link_BETA1-4 : bond 0.00565 / 0.37 ( 33) link_BETA1-4 : angle 1.92038 / 1.34 ( 99) link_NAG-ASN : bond 0.00768 / 0.53 ( 48) link_NAG-ASN : angle 3.38999 / 2.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 374 time to evaluate : 1.068 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: B 544 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8166 (mp) REVERT: B 617 LYS cc_start: 0.8514 (mttm) cc_final: 0.8174 (mttm) REVERT: G 164 GLU cc_start: 0.6898 (mp0) cc_final: 0.6316 (mp0) REVERT: H 29 MET cc_start: 0.6214 (tmm) cc_final: 0.4748 (tpp) REVERT: A 544 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 28 ASN cc_start: 0.8050 (t0) cc_final: 0.7571 (t0) REVERT: I 164 GLU cc_start: 0.6943 (mp0) cc_final: 0.6466 (mp0) REVERT: I 203 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8915 (pt0) REVERT: J 99 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7457 (ptt180) REVERT: J 100 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7281 (ttp80) REVERT: M 583 ILE cc_start: 0.9120 (mm) cc_final: 0.8842 (mt) REVERT: P 164 GLU cc_start: 0.6974 (mp0) cc_final: 0.6353 (mp0) REVERT: P 203 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8888 (pt0) REVERT: P 421 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8834 (mm) outliers start: 84 outliers final: 47 residues processed: 434 average time/residue: 0.1877 time to fit residues: 123.3633 Evaluate side-chains 401 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 294 ILE Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 357 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 421 ILE Chi-restraints excluded: chain P residue 454 TRP Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 86 optimal weight: 10.0000 chunk 249 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 268 optimal weight: 0.0470 chunk 140 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN A 630 GLN A 650 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.188495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147873 restraints weight = 34355.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147392 restraints weight = 28330.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148977 restraints weight = 28149.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149533 restraints weight = 20108.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149806 restraints weight = 18818.347| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26067 Z= 0.118 Angle : 0.639 17.804 35589 Z= 0.303 Chirality : 0.046 0.588 4185 Planarity : 0.004 0.045 4353 Dihedral : 4.677 34.640 3312 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.13 % Favored : 95.47 % Rotamer: Outliers : 2.11 % Allowed : 17.93 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 3003 helix: 0.56 (0.27), residues: 375 sheet: -0.83 (0.17), residues: 984 loop : -1.24 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 75 TYR 0.012 0.001 TYR P 433 PHE 0.018 0.001 PHE D 64 TRP 0.021 0.001 TRP Q 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (25926) covalent geometry : angle 0.59889 / 0.29 (35208) SS BOND : bond 0.00335 / 0.22 ( 42) SS BOND : angle 1.00725 / 0.66 ( 84) hydrogen bonds : bond 0.03363 / 2.25 ( 705) hydrogen bonds : angle 5.47218 / 3.86 ( 1941) link_ALPHA1-2 : bond 0.00276 / 0.15 ( 3) link_ALPHA1-2 : angle 1.47490 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00373 / 0.25 ( 9) link_ALPHA1-3 : angle 1.84524 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00255 / 0.16 ( 6) link_ALPHA1-6 : angle 1.35678 / 0.93 ( 18) link_BETA1-4 : bond 0.00531 / 0.35 ( 33) link_BETA1-4 : angle 1.57502 / 1.09 ( 99) link_NAG-ASN : bond 0.00615 / 0.44 ( 48) link_NAG-ASN : angle 3.14596 / 2.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 0.905 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: B 617 LYS cc_start: 0.8654 (mttm) cc_final: 0.8330 (mttm) REVERT: G 164 GLU cc_start: 0.6943 (mp0) cc_final: 0.6468 (mp0) REVERT: G 203 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8737 (pt0) REVERT: A 544 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7823 (mp) REVERT: C 28 ASN cc_start: 0.8105 (t0) cc_final: 0.7673 (p0) REVERT: I 164 GLU cc_start: 0.6835 (mp0) cc_final: 0.6380 (mp0) REVERT: J 99 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7473 (ptt180) REVERT: J 100 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7324 (ttp80) REVERT: K 36 TYR cc_start: 0.7574 (m-80) cc_final: 0.7263 (m-10) REVERT: M 583 ILE cc_start: 0.8984 (mm) cc_final: 0.8669 (mt) REVERT: N 62 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7387 (ttp-170) REVERT: P 164 GLU cc_start: 0.6912 (mp0) cc_final: 0.6235 (mp0) REVERT: P 203 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8733 (pt0) REVERT: R 15 LEU cc_start: 0.4921 (mm) cc_final: 0.4715 (tp) outliers start: 56 outliers final: 42 residues processed: 409 average time/residue: 0.1866 time to fit residues: 114.9880 Evaluate side-chains 401 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 294 ILE Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 169 optimal weight: 0.0670 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 136 optimal weight: 0.2980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 650 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 630 GLN I 279 ASN K 52 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.191371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151265 restraints weight = 34381.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151455 restraints weight = 27996.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153102 restraints weight = 26860.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153338 restraints weight = 19681.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153660 restraints weight = 18234.268| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26067 Z= 0.102 Angle : 0.605 17.882 35589 Z= 0.288 Chirality : 0.045 0.522 4185 Planarity : 0.004 0.057 4353 Dihedral : 4.464 31.525 3312 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.16 % Favored : 95.47 % Rotamer: Outliers : 1.77 % Allowed : 18.46 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3003 helix: 0.87 (0.28), residues: 372 sheet: -0.64 (0.18), residues: 900 loop : -1.18 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 417 TYR 0.016 0.001 TYR I 173 PHE 0.018 0.001 PHE D 64 TRP 0.024 0.001 TRP Q 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25926) covalent geometry : angle 0.56880 / 0.28 (35208) SS BOND : bond 0.00292 / 0.19 ( 42) SS BOND : angle 0.84123 / 0.56 ( 84) hydrogen bonds : bond 0.03048 / 2.04 ( 705) hydrogen bonds : angle 5.20375 / 3.66 ( 1941) link_ALPHA1-2 : bond 0.00374 / 0.21 ( 3) link_ALPHA1-2 : angle 1.44136 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00447 / 0.30 ( 9) link_ALPHA1-3 : angle 1.75441 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00341 / 0.22 ( 6) link_ALPHA1-6 : angle 1.37836 / 0.93 ( 18) link_BETA1-4 : bond 0.00576 / 0.38 ( 33) link_BETA1-4 : angle 1.48598 / 1.04 ( 99) link_NAG-ASN : bond 0.00622 / 0.45 ( 48) link_NAG-ASN : angle 2.91246 / 1.95 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 382 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 610 TRP cc_start: 0.6784 (t-100) cc_final: 0.6577 (t60) REVERT: B 617 LYS cc_start: 0.8635 (mttm) cc_final: 0.8241 (mttm) REVERT: D 51 MET cc_start: 0.8000 (tmm) cc_final: 0.7722 (tmm) REVERT: G 164 GLU cc_start: 0.6861 (mp0) cc_final: 0.6477 (mp0) REVERT: G 203 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8665 (pt0) REVERT: H 29 MET cc_start: 0.6704 (tmm) cc_final: 0.4831 (tpp) REVERT: C 28 ASN cc_start: 0.8064 (t0) cc_final: 0.7788 (p0) REVERT: I 164 GLU cc_start: 0.6768 (mp0) cc_final: 0.6440 (mp0) REVERT: J 100 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7336 (ttp80) REVERT: M 583 ILE cc_start: 0.8938 (mm) cc_final: 0.8594 (mt) REVERT: N 62 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7304 (ttp-170) REVERT: P 164 GLU cc_start: 0.6792 (mp0) cc_final: 0.6124 (mp0) outliers start: 47 outliers final: 34 residues processed: 414 average time/residue: 0.1880 time to fit residues: 117.1367 Evaluate side-chains 393 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 358 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 647 GLU Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 189 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.190545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150217 restraints weight = 34262.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149491 restraints weight = 27499.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151029 restraints weight = 27475.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151719 restraints weight = 20124.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151901 restraints weight = 19003.392| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26067 Z= 0.118 Angle : 0.618 16.895 35589 Z= 0.293 Chirality : 0.046 0.519 4185 Planarity : 0.004 0.046 4353 Dihedral : 4.426 30.395 3312 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.26 % Favored : 95.34 % Rotamer: Outliers : 1.77 % Allowed : 19.17 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3003 helix: 0.82 (0.28), residues: 372 sheet: -0.51 (0.17), residues: 933 loop : -1.16 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 542 TYR 0.018 0.001 TYR I 173 PHE 0.019 0.001 PHE D 64 TRP 0.037 0.001 TRP Q 36 HIS 0.003 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (25926) covalent geometry : angle 0.58253 / 0.29 (35208) SS BOND : bond 0.00304 / 0.20 ( 42) SS BOND : angle 0.81961 / 0.54 ( 84) hydrogen bonds : bond 0.03134 / 2.10 ( 705) hydrogen bonds : angle 5.12751 / 3.59 ( 1941) link_ALPHA1-2 : bond 0.00320 / 0.18 ( 3) link_ALPHA1-2 : angle 1.49976 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00405 / 0.28 ( 9) link_ALPHA1-3 : angle 1.76518 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00292 / 0.19 ( 6) link_ALPHA1-6 : angle 1.39416 / 0.94 ( 18) link_BETA1-4 : bond 0.00536 / 0.35 ( 33) link_BETA1-4 : angle 1.54768 / 1.08 ( 99) link_NAG-ASN : bond 0.00629 / 0.45 ( 48) link_NAG-ASN : angle 2.89749 / 1.95 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 0.912 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: B 584 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 610 TRP cc_start: 0.6969 (t-100) cc_final: 0.6720 (t60) REVERT: B 617 LYS cc_start: 0.8674 (mttm) cc_final: 0.8262 (mttm) REVERT: D 51 MET cc_start: 0.8046 (tmm) cc_final: 0.7737 (tmm) REVERT: G 164 GLU cc_start: 0.6860 (mp0) cc_final: 0.6452 (mp0) REVERT: G 203 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8731 (pt0) REVERT: A 638 TYR cc_start: 0.6694 (p90) cc_final: 0.6357 (p90) REVERT: A 663 LEU cc_start: 0.7348 (mt) cc_final: 0.6996 (mt) REVERT: I 164 GLU cc_start: 0.6828 (mp0) cc_final: 0.6435 (mp0) REVERT: I 203 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: J 100 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7327 (ttp80) REVERT: J 119 MET cc_start: 0.6369 (mtt) cc_final: 0.6110 (ptp) REVERT: M 583 ILE cc_start: 0.8942 (mm) cc_final: 0.8572 (mt) REVERT: N 62 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7354 (ttp-170) REVERT: P 164 GLU cc_start: 0.6821 (mp0) cc_final: 0.6107 (mp0) REVERT: P 203 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8740 (pt0) outliers start: 47 outliers final: 36 residues processed: 399 average time/residue: 0.1799 time to fit residues: 109.2921 Evaluate side-chains 396 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 33 optimal weight: 8.9990 chunk 239 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 241 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151521 restraints weight = 33796.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150761 restraints weight = 30617.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152476 restraints weight = 27050.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153104 restraints weight = 18910.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153427 restraints weight = 17876.347| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26067 Z= 0.110 Angle : 0.610 17.123 35589 Z= 0.290 Chirality : 0.045 0.510 4185 Planarity : 0.004 0.045 4353 Dihedral : 4.373 29.822 3312 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.13 % Favored : 95.47 % Rotamer: Outliers : 1.66 % Allowed : 19.32 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3003 helix: 0.82 (0.28), residues: 375 sheet: -0.54 (0.18), residues: 900 loop : -1.12 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 542 TYR 0.018 0.001 TYR I 173 PHE 0.019 0.001 PHE F 58 TRP 0.036 0.001 TRP Q 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25926) covalent geometry : angle 0.57620 / 0.28 (35208) SS BOND : bond 0.00298 / 0.19 ( 42) SS BOND : angle 0.81366 / 0.54 ( 84) hydrogen bonds : bond 0.03058 / 2.06 ( 705) hydrogen bonds : angle 5.06139 / 3.54 ( 1941) link_ALPHA1-2 : bond 0.00367 / 0.20 ( 3) link_ALPHA1-2 : angle 1.47867 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00417 / 0.28 ( 9) link_ALPHA1-3 : angle 1.77177 / 1.07 ( 27) link_ALPHA1-6 : bond 0.00324 / 0.21 ( 6) link_ALPHA1-6 : angle 1.38910 / 0.94 ( 18) link_BETA1-4 : bond 0.00557 / 0.37 ( 33) link_BETA1-4 : angle 1.49716 / 1.05 ( 99) link_NAG-ASN : bond 0.00619 / 0.45 ( 48) link_NAG-ASN : angle 2.83406 / 1.90 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 369 time to evaluate : 0.930 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: B 584 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 610 TRP cc_start: 0.7039 (t-100) cc_final: 0.6793 (t60) REVERT: B 617 LYS cc_start: 0.8632 (mttm) cc_final: 0.8256 (mttm) REVERT: D 28 ASN cc_start: 0.8134 (t0) cc_final: 0.7527 (p0) REVERT: D 51 MET cc_start: 0.8021 (tmm) cc_final: 0.7725 (tmm) REVERT: G 164 GLU cc_start: 0.6847 (mp0) cc_final: 0.6466 (mp0) REVERT: G 203 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8711 (pt0) REVERT: H 29 MET cc_start: 0.6650 (tmm) cc_final: 0.4524 (tpp) REVERT: A 535 MET cc_start: 0.7033 (ttt) cc_final: 0.6795 (ttm) REVERT: A 638 TYR cc_start: 0.6659 (p90) cc_final: 0.6350 (p90) REVERT: A 647 GLU cc_start: 0.8037 (tt0) cc_final: 0.7803 (tt0) REVERT: A 663 LEU cc_start: 0.7365 (mt) cc_final: 0.7016 (mt) REVERT: I 164 GLU cc_start: 0.6805 (mp0) cc_final: 0.6406 (mp0) REVERT: I 203 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8688 (pt0) REVERT: J 100 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7336 (ttp80) REVERT: M 583 ILE cc_start: 0.8926 (mm) cc_final: 0.8523 (mt) REVERT: N 62 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7337 (ttp-170) REVERT: P 164 GLU cc_start: 0.6853 (mp0) cc_final: 0.6160 (mp0) REVERT: P 203 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8718 (pt0) REVERT: P 417 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7601 (mtp85) REVERT: Q 99 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7185 (ptm-80) outliers start: 44 outliers final: 37 residues processed: 396 average time/residue: 0.1838 time to fit residues: 110.8928 Evaluate side-chains 402 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 361 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 424 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 158 SER Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 0.0770 chunk 105 optimal weight: 0.3980 chunk 185 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 231 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN A 543 GLN I 279 ASN M 543 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151432 restraints weight = 33735.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149805 restraints weight = 29242.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151625 restraints weight = 26499.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152318 restraints weight = 19326.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152656 restraints weight = 18302.472| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26067 Z= 0.108 Angle : 0.604 16.476 35589 Z= 0.287 Chirality : 0.045 0.503 4185 Planarity : 0.004 0.055 4353 Dihedral : 4.326 29.059 3312 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.13 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 19.25 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.21 % 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: -0.91 (0.15), residues: 3003 helix: 0.92 (0.28), residues: 372 sheet: -0.29 (0.17), residues: 915 loop : -1.13 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 542 TYR 0.018 0.001 TYR I 173 PHE 0.018 0.001 PHE D 64 TRP 0.033 0.001 TRP Q 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (25926) covalent geometry : angle 0.57038 / 0.28 (35208) SS BOND : bond 0.00286 / 0.19 ( 42) SS BOND : angle 0.80075 / 0.53 ( 84) hydrogen bonds : bond 0.03047 / 2.04 ( 705) hydrogen bonds : angle 4.99979 / 3.49 ( 1941) link_ALPHA1-2 : bond 0.00367 / 0.20 ( 3) link_ALPHA1-2 : angle 1.47811 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00420 / 0.29 ( 9) link_ALPHA1-3 : angle 1.76783 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00312 / 0.20 ( 6) link_ALPHA1-6 : angle 1.37828 / 0.93 ( 18) link_BETA1-4 : bond 0.00550 / 0.36 ( 33) link_BETA1-4 : angle 1.49219 / 1.05 ( 99) link_NAG-ASN : bond 0.00605 / 0.44 ( 48) link_NAG-ASN : angle 2.77268 / 1.86 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.23 seconds wall clock time: 71 minutes 2.05 seconds (4262.05 seconds total)