Starting phenix.real_space_refine on Fri Feb 6 11:47:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ucg_26443/02_2026/7ucg_26443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ucg_26443/02_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_26443/02_2026/7ucg_26443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ucg_26443/02_2026/7ucg_26443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ucg_26443/02_2026/7ucg_26443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ucg_26443/02_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-2.0-5952/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 21 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.46, per 1000 atoms: 0.25 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: 2.71 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: 1.24 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: 5.77 Time building geometry restraints manager: 3.36 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 - 22.33: 15434 22.33 - 44.65: 1027 44.65 - 66.98: 143 66.98 - 89.30: 94 89.30 - 111.63: 39 Dihedral angle restraints: 16737 sinusoidal: 7932 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 16734 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.010 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 16.136 111.628 10965 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 covalent geometry : bond 0.00545 (25926) covalent geometry : angle 0.97645 (35208) SS BOND : bond 0.00489 ( 42) SS BOND : angle 1.23430 ( 84) hydrogen bonds : bond 0.28168 ( 705) hydrogen bonds : angle 10.66897 ( 1941) link_ALPHA1-2 : bond 0.00316 ( 3) link_ALPHA1-2 : angle 1.70710 ( 9) link_ALPHA1-3 : bond 0.00419 ( 9) link_ALPHA1-3 : angle 2.28833 ( 27) link_ALPHA1-6 : bond 0.00333 ( 6) link_ALPHA1-6 : angle 1.70237 ( 18) link_BETA1-4 : bond 0.01033 ( 33) link_BETA1-4 : angle 2.82197 ( 99) link_NAG-ASN : bond 0.00997 ( 48) link_NAG-ASN : angle 5.61265 ( 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 : 0.981 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: 0.2097 time to fit residues: 182.7514 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 : 0.960 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN C 39 GLN I 170 GLN J 102 GLN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.207940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.171854 restraints weight = 34701.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172750 restraints weight = 32230.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173908 restraints weight = 28110.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174590 restraints weight = 20436.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174748 restraints weight = 19384.807| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1685 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= 0.133 Angle : 0.718 20.661 35589 Z= 0.344 Chirality : 0.050 0.928 4185 Planarity : 0.005 0.066 4353 Dihedral : 12.139 95.394 5343 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.10 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 9.53 % Favored : 88.85 % 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: -1.97 (0.14), residues: 3003 helix: -0.64 (0.25), residues: 369 sheet: -0.91 (0.16), residues: 936 loop : -1.71 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 417 TYR 0.016 0.001 TYR M 638 PHE 0.009 0.001 PHE P 233 TRP 0.019 0.001 TRP B 610 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00281 (25926) covalent geometry : angle 0.65930 (35208) SS BOND : bond 0.00296 ( 42) SS BOND : angle 0.78861 ( 84) hydrogen bonds : bond 0.05280 ( 705) hydrogen bonds : angle 7.13920 ( 1941) link_ALPHA1-2 : bond 0.00495 ( 3) link_ALPHA1-2 : angle 1.42974 ( 9) link_ALPHA1-3 : bond 0.00834 ( 9) link_ALPHA1-3 : angle 1.53491 ( 27) link_ALPHA1-6 : bond 0.00453 ( 6) link_ALPHA1-6 : angle 1.88998 ( 18) link_BETA1-4 : bond 0.00413 ( 33) link_BETA1-4 : angle 2.06614 ( 99) link_NAG-ASN : bond 0.00781 ( 48) link_NAG-ASN : angle 4.11656 ( 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 478 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 435 time to evaluate : 0.952 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: 0.6438 (ttp) cc_final: 0.5627 (mtt) REVERT: B 573 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6650 (tp) REVERT: B 617 LYS cc_start: 0.8503 (mttm) cc_final: 0.8144 (mttm) REVERT: A 573 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6817 (tp) REVERT: A 641 THR cc_start: 0.8002 (t) cc_final: 0.7598 (m) REVERT: A 651 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7746 (t0) REVERT: C 10 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6171 (mt-10) REVERT: C 28 ASN cc_start: 0.7778 (t0) cc_final: 0.7500 (t0) REVERT: C 39 GLN cc_start: 0.5740 (tt0) cc_final: 0.5518 (tt0) REVERT: F 49 ARG cc_start: 0.7394 (ttm170) cc_final: 0.6909 (mtp180) REVERT: I 164 GLU cc_start: 0.6608 (mp0) cc_final: 0.6174 (mp0) REVERT: I 334 SER cc_start: 0.6649 (OUTLIER) cc_final: 0.6354 (m) REVERT: I 362 SER cc_start: 0.7983 (t) cc_final: 0.7754 (t) REVERT: J 99 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7071 (ptt180) REVERT: M 535 MET cc_start: 0.7038 (ttm) cc_final: 0.6003 (mtt) REVERT: M 573 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6987 (tp) REVERT: M 644 ARG cc_start: 0.7392 (mmt-90) cc_final: 0.7056 (mmt180) outliers start: 43 outliers final: 27 residues processed: 457 average time/residue: 0.2168 time to fit residues: 147.1600 Evaluate side-chains 420 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 387 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 230 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 201 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 236 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4321 r_free = 0.4321 target = 0.203963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166998 restraints weight = 34640.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166104 restraints weight = 34729.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167999 restraints weight = 32092.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168796 restraints weight = 22043.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169055 restraints weight = 21529.910| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26067 Z= 0.133 Angle : 0.673 19.501 35589 Z= 0.320 Chirality : 0.049 0.865 4185 Planarity : 0.004 0.052 4353 Dihedral : 10.998 92.273 5343 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.20 % Favored : 95.47 % Rotamer: Outliers : 2.11 % Allowed : 12.88 % Favored : 85.01 % 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: -1.52 (0.15), residues: 3003 helix: 0.11 (0.27), residues: 369 sheet: -0.63 (0.17), residues: 888 loop : -1.49 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 417 TYR 0.012 0.001 TYR I 382 PHE 0.021 0.001 PHE D 64 TRP 0.035 0.002 TRP B 610 HIS 0.005 0.001 HIS R 38 Details of bonding type rmsd covalent geometry : bond 0.00293 (25926) covalent geometry : angle 0.62090 (35208) SS BOND : bond 0.00331 ( 42) SS BOND : angle 0.92166 ( 84) hydrogen bonds : bond 0.04093 ( 705) hydrogen bonds : angle 6.19642 ( 1941) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.48753 ( 9) link_ALPHA1-3 : bond 0.00832 ( 9) link_ALPHA1-3 : angle 1.60116 ( 27) link_ALPHA1-6 : bond 0.00442 ( 6) link_ALPHA1-6 : angle 1.77267 ( 18) link_BETA1-4 : bond 0.00430 ( 33) link_BETA1-4 : angle 1.82641 ( 99) link_NAG-ASN : bond 0.00903 ( 48) link_NAG-ASN : angle 3.70350 ( 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 462 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 406 time to evaluate : 0.997 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: 0.6472 (ttp) cc_final: 0.5657 (mtt) REVERT: B 544 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7487 (mp) REVERT: B 617 LYS cc_start: 0.8543 (mttm) cc_final: 0.8113 (mttm) REVERT: H 100 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: L 93 MET cc_start: 0.7582 (ttt) cc_final: 0.7355 (ttt) REVERT: A 641 THR cc_start: 0.8001 (t) cc_final: 0.7579 (m) REVERT: A 644 ARG cc_start: 0.7411 (mmt-90) cc_final: 0.7151 (mmt180) REVERT: F 49 ARG cc_start: 0.7425 (ttm170) cc_final: 0.6910 (mtp180) REVERT: I 164 GLU cc_start: 0.6477 (mp0) cc_final: 0.5804 (mp0) REVERT: I 444 LYS cc_start: 0.7326 (tptt) cc_final: 0.7076 (mptt) REVERT: J 99 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7179 (ptt180) REVERT: M 583 ILE cc_start: 0.9060 (mm) cc_final: 0.8760 (mt) REVERT: M 644 ARG cc_start: 0.7448 (mmt-90) cc_final: 0.7188 (mmt180) REVERT: P 432 MET cc_start: 0.8491 (ptm) cc_final: 0.8104 (ptp) outliers start: 56 outliers final: 33 residues processed: 436 average time/residue: 0.2097 time to fit residues: 136.8616 Evaluate side-chains 397 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 362 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 342 LEU 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 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 342 LEU Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 99 ARG 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 36 VAL 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 363 SER Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 392 THR 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: 5.9990 chunk 249 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 236 optimal weight: 0.0470 chunk 162 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 228 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 136 optimal weight: 0.0980 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN G 258 GLN K 50 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.201488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164206 restraints weight = 34173.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163255 restraints weight = 34684.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164971 restraints weight = 32111.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165608 restraints weight = 22956.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166158 restraints weight = 22185.313| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26067 Z= 0.132 Angle : 0.661 18.832 35589 Z= 0.312 Chirality : 0.048 0.829 4185 Planarity : 0.004 0.048 4353 Dihedral : 10.433 88.691 5343 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.26 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 13.94 % Favored : 83.80 % 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: -1.42 (0.15), residues: 3003 helix: 0.35 (0.27), residues: 375 sheet: -0.70 (0.17), residues: 906 loop : -1.39 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 8 TYR 0.011 0.001 TYR M 638 PHE 0.012 0.001 PHE D 64 TRP 0.021 0.001 TRP D 113 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00293 (25926) covalent geometry : angle 0.61030 (35208) SS BOND : bond 0.00298 ( 42) SS BOND : angle 0.83938 ( 84) hydrogen bonds : bond 0.03654 ( 705) hydrogen bonds : angle 5.83071 ( 1941) link_ALPHA1-2 : bond 0.00348 ( 3) link_ALPHA1-2 : angle 1.54038 ( 9) link_ALPHA1-3 : bond 0.00782 ( 9) link_ALPHA1-3 : angle 1.65034 ( 27) link_ALPHA1-6 : bond 0.00461 ( 6) link_ALPHA1-6 : angle 1.87529 ( 18) link_BETA1-4 : bond 0.00407 ( 33) link_BETA1-4 : angle 1.84763 ( 99) link_NAG-ASN : bond 0.00649 ( 48) link_NAG-ASN : angle 3.59996 ( 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 460 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 400 time to evaluate : 1.081 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: 0.7948 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 617 LYS cc_start: 0.8528 (mttm) cc_final: 0.8246 (mttm) REVERT: B 647 GLU cc_start: 0.7889 (tt0) cc_final: 0.7613 (tt0) REVERT: H 29 MET cc_start: 0.2487 (mmt) cc_final: 0.2272 (tmm) REVERT: H 85 VAL cc_start: 0.5824 (m) cc_final: 0.5411 (t) REVERT: L 93 MET cc_start: 0.7615 (ttt) cc_final: 0.7407 (ttt) REVERT: A 641 THR cc_start: 0.8144 (t) cc_final: 0.7671 (m) REVERT: A 647 GLU cc_start: 0.7875 (tt0) cc_final: 0.7673 (tt0) REVERT: C 28 ASN cc_start: 0.7824 (t0) cc_final: 0.7560 (t0) REVERT: C 95 TYR cc_start: 0.7300 (m-80) cc_final: 0.6944 (m-80) REVERT: I 164 GLU cc_start: 0.6460 (mp0) cc_final: 0.5729 (mp0) REVERT: J 99 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7319 (ptt180) REVERT: J 100 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7175 (ttp80) REVERT: M 583 ILE cc_start: 0.9037 (mm) cc_final: 0.8696 (mt) REVERT: M 644 ARG cc_start: 0.7358 (mmt-90) cc_final: 0.7100 (mmt180) outliers start: 60 outliers final: 39 residues processed: 432 average time/residue: 0.2052 time to fit residues: 133.4304 Evaluate side-chains 398 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 357 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 38 VAL Chi-restraints excluded: chain G residue 125 LEU 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 L residue 75 THR 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 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 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 647 GLU Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 36 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 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 Q residue 121 VAL 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: 0.6980 chunk 204 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN G 344 GLN A 650 GLN F 34 GLN K 50 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN O 35 HIS ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.201655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164324 restraints weight = 34262.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163329 restraints weight = 36433.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165037 restraints weight = 33485.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165793 restraints weight = 23273.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165911 restraints weight = 21685.040| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26067 Z= 0.136 Angle : 0.649 18.365 35589 Z= 0.308 Chirality : 0.048 0.808 4185 Planarity : 0.004 0.047 4353 Dihedral : 10.033 85.117 5343 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % Favored : 81.96 % 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: -1.35 (0.15), residues: 3003 helix: 0.49 (0.27), residues: 375 sheet: -0.70 (0.17), residues: 912 loop : -1.32 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 49 TYR 0.015 0.001 TYR B 638 PHE 0.013 0.001 PHE D 64 TRP 0.019 0.001 TRP J 36 HIS 0.005 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00307 (25926) covalent geometry : angle 0.60028 (35208) SS BOND : bond 0.00308 ( 42) SS BOND : angle 0.83251 ( 84) hydrogen bonds : bond 0.03498 ( 705) hydrogen bonds : angle 5.59887 ( 1941) link_ALPHA1-2 : bond 0.00328 ( 3) link_ALPHA1-2 : angle 1.57267 ( 9) link_ALPHA1-3 : bond 0.00743 ( 9) link_ALPHA1-3 : angle 1.69366 ( 27) link_ALPHA1-6 : bond 0.00466 ( 6) link_ALPHA1-6 : angle 1.87626 ( 18) link_BETA1-4 : bond 0.00441 ( 33) link_BETA1-4 : angle 1.81837 ( 99) link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 3.47539 ( 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 462 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 0.979 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: 0.8085 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 617 LYS cc_start: 0.8492 (mttm) cc_final: 0.8203 (mttm) REVERT: H 29 MET cc_start: 0.3105 (mmt) cc_final: 0.2472 (tmm) REVERT: A 641 THR cc_start: 0.8207 (t) cc_final: 0.7652 (m) REVERT: F 49 ARG cc_start: 0.7489 (ttm170) cc_final: 0.7156 (mtt90) REVERT: I 164 GLU cc_start: 0.6680 (mp0) cc_final: 0.5837 (mp0) REVERT: I 334 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6971 (m) REVERT: J 99 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7329 (ptt180) REVERT: J 100 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7178 (ttp80) REVERT: M 583 ILE cc_start: 0.9068 (mm) cc_final: 0.8730 (mt) REVERT: M 644 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.7050 (mmt180) REVERT: P 164 GLU cc_start: 0.6737 (mp0) cc_final: 0.6178 (mp0) outliers start: 73 outliers final: 51 residues processed: 431 average time/residue: 0.2045 time to fit residues: 131.7723 Evaluate side-chains 414 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 360 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR 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 38 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 84 CYS 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 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 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 647 GLU Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 36 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 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 75 THR 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: 4.9990 chunk 125 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 260 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 266 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 221 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN A 630 GLN F 34 GLN I 344 GLN K 50 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 344 GLN R 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.162184 restraints weight = 34212.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160782 restraints weight = 35257.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162731 restraints weight = 32503.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163483 restraints weight = 22768.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163682 restraints weight = 21510.862| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26067 Z= 0.119 Angle : 0.629 17.847 35589 Z= 0.297 Chirality : 0.047 0.766 4185 Planarity : 0.004 0.058 4353 Dihedral : 9.676 82.150 5343 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.13 % Favored : 95.50 % Rotamer: Outliers : 2.75 % Allowed : 15.93 % Favored : 81.32 % 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: -1.22 (0.15), residues: 3003 helix: 0.65 (0.28), residues: 375 sheet: -0.63 (0.17), residues: 912 loop : -1.25 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 417 TYR 0.013 0.001 TYR B 638 PHE 0.012 0.001 PHE C 29 TRP 0.022 0.001 TRP Q 36 HIS 0.005 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00264 (25926) covalent geometry : angle 0.58275 (35208) SS BOND : bond 0.00293 ( 42) SS BOND : angle 0.80533 ( 84) hydrogen bonds : bond 0.03292 ( 705) hydrogen bonds : angle 5.42920 ( 1941) link_ALPHA1-2 : bond 0.00381 ( 3) link_ALPHA1-2 : angle 1.51033 ( 9) link_ALPHA1-3 : bond 0.00713 ( 9) link_ALPHA1-3 : angle 1.68515 ( 27) link_ALPHA1-6 : bond 0.00523 ( 6) link_ALPHA1-6 : angle 1.88755 ( 18) link_BETA1-4 : bond 0.00456 ( 33) link_BETA1-4 : angle 1.77758 ( 99) link_NAG-ASN : bond 0.00642 ( 48) link_NAG-ASN : angle 3.33613 ( 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 460 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 387 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 544 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 617 LYS cc_start: 0.8480 (mttm) cc_final: 0.7969 (mtpt) REVERT: H 29 MET cc_start: 0.3425 (mmt) cc_final: 0.2745 (tmm) REVERT: H 33 TYR cc_start: 0.6540 (m-80) cc_final: 0.6021 (m-80) REVERT: A 647 GLU cc_start: 0.8023 (tt0) cc_final: 0.7816 (tt0) REVERT: C 28 ASN cc_start: 0.7940 (t0) cc_final: 0.7123 (p0) REVERT: F 49 ARG cc_start: 0.7455 (ttm170) cc_final: 0.7117 (mtt90) REVERT: I 164 GLU cc_start: 0.6776 (mp0) cc_final: 0.5945 (mp0) REVERT: I 334 SER cc_start: 0.7239 (OUTLIER) cc_final: 0.7014 (m) REVERT: J 85 VAL cc_start: 0.6597 (m) cc_final: 0.6080 (t) REVERT: J 99 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7426 (ptt180) REVERT: M 583 ILE cc_start: 0.9000 (mm) cc_final: 0.8672 (mt) REVERT: P 164 GLU cc_start: 0.6677 (mp0) cc_final: 0.6018 (mp0) outliers start: 73 outliers final: 53 residues processed: 429 average time/residue: 0.2011 time to fit residues: 130.2379 Evaluate side-chains 419 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 363 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 647 GLU 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 38 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 125 LEU 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 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 497 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 84 CYS 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 422 ILE Chi-restraints excluded: chain I residue 424 MET 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 K residue 75 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 68 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 363 SER Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 75 THR 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: 4.9990 chunk 64 optimal weight: 3.9990 chunk 183 optimal weight: 0.0040 chunk 288 optimal weight: 7.9990 chunk 127 optimal weight: 0.0270 chunk 101 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 276 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 34 GLN I 279 ASN K 50 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.201611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164564 restraints weight = 34189.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163147 restraints weight = 36153.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165045 restraints weight = 32941.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165708 restraints weight = 23322.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165851 restraints weight = 22153.093| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26067 Z= 0.103 Angle : 0.619 18.287 35589 Z= 0.291 Chirality : 0.047 0.745 4185 Planarity : 0.004 0.046 4353 Dihedral : 9.377 79.817 5343 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.10 % Favored : 95.54 % Rotamer: Outliers : 2.22 % Allowed : 17.36 % Favored : 80.41 % 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: -1.11 (0.15), residues: 3003 helix: 0.76 (0.28), residues: 375 sheet: -0.46 (0.18), residues: 888 loop : -1.24 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 417 TYR 0.015 0.001 TYR J 94 PHE 0.011 0.001 PHE C 29 TRP 0.027 0.001 TRP H 36 HIS 0.003 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00223 (25926) covalent geometry : angle 0.57261 (35208) SS BOND : bond 0.00275 ( 42) SS BOND : angle 0.75825 ( 84) hydrogen bonds : bond 0.03092 ( 705) hydrogen bonds : angle 5.30123 ( 1941) link_ALPHA1-2 : bond 0.00425 ( 3) link_ALPHA1-2 : angle 1.45324 ( 9) link_ALPHA1-3 : bond 0.00780 ( 9) link_ALPHA1-3 : angle 1.71542 ( 27) link_ALPHA1-6 : bond 0.00590 ( 6) link_ALPHA1-6 : angle 1.87326 ( 18) link_BETA1-4 : bond 0.00476 ( 33) link_BETA1-4 : angle 1.72675 ( 99) link_NAG-ASN : bond 0.00607 ( 48) link_NAG-ASN : angle 3.30217 ( 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 433 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 0.785 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: 0.8094 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 617 LYS cc_start: 0.8450 (mttm) cc_final: 0.7945 (mtpt) REVERT: D 51 MET cc_start: 0.7852 (tmm) cc_final: 0.7628 (tmm) REVERT: G 164 GLU cc_start: 0.6932 (mp0) cc_final: 0.6522 (mp0) REVERT: H 29 MET cc_start: 0.3731 (mmt) cc_final: 0.2888 (tmm) REVERT: A 641 THR cc_start: 0.8196 (t) cc_final: 0.7616 (m) REVERT: C 28 ASN cc_start: 0.8109 (t0) cc_final: 0.7519 (p0) REVERT: F 49 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7107 (mtt90) REVERT: I 164 GLU cc_start: 0.6679 (mp0) cc_final: 0.5839 (mp0) REVERT: I 334 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.7119 (m) REVERT: J 100 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7059 (ttp80) REVERT: M 583 ILE cc_start: 0.8943 (mm) cc_final: 0.8603 (mt) REVERT: P 164 GLU cc_start: 0.6657 (mp0) cc_final: 0.5997 (mp0) REVERT: P 417 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7489 (mtp85) outliers start: 59 outliers final: 41 residues processed: 412 average time/residue: 0.1924 time to fit residues: 118.2320 Evaluate side-chains 400 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 357 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain D residue 118 MET 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 125 LEU Chi-restraints excluded: chain G residue 163 THR 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 497 LYS Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 84 CYS 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 163 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 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 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 163 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 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: 2.9990 chunk 263 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 169 optimal weight: 0.0270 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 136 optimal weight: 0.0040 overall best weight: 0.4450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN K 50 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.201458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164511 restraints weight = 34312.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163145 restraints weight = 35937.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165065 restraints weight = 32218.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165749 restraints weight = 22755.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165894 restraints weight = 21599.739| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26067 Z= 0.104 Angle : 0.614 16.908 35589 Z= 0.288 Chirality : 0.047 0.712 4185 Planarity : 0.004 0.046 4353 Dihedral : 9.038 76.478 5343 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 17.70 % Favored : 79.96 % 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: -1.02 (0.15), residues: 3003 helix: 0.84 (0.28), residues: 375 sheet: -0.43 (0.17), residues: 897 loop : -1.15 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 75 TYR 0.016 0.001 TYR I 173 PHE 0.013 0.001 PHE E 58 TRP 0.024 0.001 TRP H 36 HIS 0.003 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00225 (25926) covalent geometry : angle 0.57075 (35208) SS BOND : bond 0.00273 ( 42) SS BOND : angle 0.70983 ( 84) hydrogen bonds : bond 0.03015 ( 705) hydrogen bonds : angle 5.11599 ( 1941) link_ALPHA1-2 : bond 0.00433 ( 3) link_ALPHA1-2 : angle 1.45730 ( 9) link_ALPHA1-3 : bond 0.00800 ( 9) link_ALPHA1-3 : angle 1.70470 ( 27) link_ALPHA1-6 : bond 0.00648 ( 6) link_ALPHA1-6 : angle 1.86384 ( 18) link_BETA1-4 : bond 0.00481 ( 33) link_BETA1-4 : angle 1.74943 ( 99) link_NAG-ASN : bond 0.00622 ( 48) link_NAG-ASN : angle 3.17162 ( 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 430 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 0.865 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: 0.8443 (mttm) cc_final: 0.7968 (mtpt) REVERT: D 51 MET cc_start: 0.7863 (tmm) cc_final: 0.7643 (tmm) REVERT: G 164 GLU cc_start: 0.6766 (mp0) cc_final: 0.6361 (mp0) REVERT: G 211 ASP cc_start: 0.7951 (t0) cc_final: 0.7698 (t70) REVERT: H 29 MET cc_start: 0.3770 (mmt) cc_final: 0.2942 (tmm) REVERT: A 544 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 641 THR cc_start: 0.8192 (t) cc_final: 0.7602 (m) REVERT: C 28 ASN cc_start: 0.7997 (t0) cc_final: 0.7632 (p0) REVERT: F 49 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7072 (mtt90) REVERT: I 164 GLU cc_start: 0.6599 (mp0) cc_final: 0.5768 (mp0) REVERT: J 33 TYR cc_start: 0.6617 (m-80) cc_final: 0.6269 (m-80) REVERT: J 100 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7046 (ttp80) REVERT: M 583 ILE cc_start: 0.8942 (mm) cc_final: 0.8608 (mt) REVERT: P 164 GLU cc_start: 0.6693 (mp0) cc_final: 0.6029 (mp0) REVERT: P 417 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7490 (mtp85) outliers start: 62 outliers final: 48 residues processed: 411 average time/residue: 0.1916 time to fit residues: 118.2981 Evaluate side-chains 406 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 THR 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 125 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 242 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 497 LYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR 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 F residue 71 ILE Chi-restraints excluded: chain F residue 84 CYS 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 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 M residue 606 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 44 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 323 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 189 optimal weight: 20.0000 chunk 197 optimal weight: 0.0040 chunk 8 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 274 optimal weight: 0.0970 chunk 140 optimal weight: 0.7980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN F 34 GLN I 352 HIS K 50 ASN ** 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 = 0.4277 r_free = 0.4277 target = 0.199552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162222 restraints weight = 34176.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160501 restraints weight = 36108.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162801 restraints weight = 33290.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162979 restraints weight = 23838.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163423 restraints weight = 22655.384| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3727 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= 0.119 Angle : 0.627 17.146 35589 Z= 0.295 Chirality : 0.047 0.737 4185 Planarity : 0.004 0.059 4353 Dihedral : 8.883 74.051 5343 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.43 % Favored : 95.20 % Rotamer: Outliers : 2.15 % Allowed : 18.04 % Favored : 79.81 % 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: -1.03 (0.15), residues: 3003 helix: 0.86 (0.28), residues: 372 sheet: -0.47 (0.17), residues: 915 loop : -1.15 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 49 TYR 0.018 0.001 TYR I 173 PHE 0.016 0.001 PHE D 64 TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00268 (25926) covalent geometry : angle 0.58314 (35208) SS BOND : bond 0.00300 ( 42) SS BOND : angle 0.74792 ( 84) hydrogen bonds : bond 0.03071 ( 705) hydrogen bonds : angle 5.06506 ( 1941) link_ALPHA1-2 : bond 0.00361 ( 3) link_ALPHA1-2 : angle 1.54711 ( 9) link_ALPHA1-3 : bond 0.00724 ( 9) link_ALPHA1-3 : angle 1.68714 ( 27) link_ALPHA1-6 : bond 0.00609 ( 6) link_ALPHA1-6 : angle 1.85639 ( 18) link_BETA1-4 : bond 0.00491 ( 33) link_BETA1-4 : angle 1.80102 ( 99) link_NAG-ASN : bond 0.00621 ( 48) link_NAG-ASN : angle 3.19466 ( 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 423 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 0.884 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 617 LYS cc_start: 0.8467 (mttm) cc_final: 0.7983 (mtpt) REVERT: D 51 MET cc_start: 0.7933 (tmm) cc_final: 0.7664 (tmm) REVERT: G 164 GLU cc_start: 0.6771 (mp0) cc_final: 0.6396 (mp0) REVERT: G 211 ASP cc_start: 0.7958 (t0) cc_final: 0.7713 (t70) REVERT: H 29 MET cc_start: 0.3912 (mmt) cc_final: 0.3019 (tmm) REVERT: H 100 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7178 (ttp80) REVERT: A 535 MET cc_start: 0.6917 (ttt) cc_final: 0.6645 (ttm) REVERT: A 544 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7863 (mp) REVERT: C 28 ASN cc_start: 0.7983 (t0) cc_final: 0.7712 (p0) REVERT: F 49 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7130 (mtt90) REVERT: I 164 GLU cc_start: 0.6626 (mp0) cc_final: 0.5793 (mp0) REVERT: J 100 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7165 (ttp80) REVERT: M 583 ILE cc_start: 0.8986 (mm) cc_final: 0.8657 (mt) REVERT: P 164 GLU cc_start: 0.6768 (mp0) cc_final: 0.6075 (mp0) REVERT: P 417 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7585 (mtp85) outliers start: 57 outliers final: 47 residues processed: 401 average time/residue: 0.1925 time to fit residues: 116.3329 Evaluate side-chains 407 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 497 LYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain C residue 31 ASP 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 F residue 84 CYS 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 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 118 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 68 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 323 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 33 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN F 34 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.200020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162554 restraints weight = 34015.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162782 restraints weight = 32264.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164301 restraints weight = 31250.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164378 restraints weight = 23323.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164759 restraints weight = 20685.998| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26067 Z= 0.113 Angle : 0.622 16.863 35589 Z= 0.293 Chirality : 0.047 0.736 4185 Planarity : 0.004 0.046 4353 Dihedral : 8.727 73.538 5343 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.33 % Favored : 95.30 % Rotamer: Outliers : 2.03 % Allowed : 18.49 % Favored : 79.47 % 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: -0.98 (0.15), residues: 3003 helix: 0.88 (0.28), residues: 372 sheet: -0.48 (0.17), residues: 942 loop : -1.08 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 542 TYR 0.017 0.001 TYR I 173 PHE 0.018 0.001 PHE F 58 TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00252 (25926) covalent geometry : angle 0.57932 (35208) SS BOND : bond 0.00289 ( 42) SS BOND : angle 0.75075 ( 84) hydrogen bonds : bond 0.03038 ( 705) hydrogen bonds : angle 5.01564 ( 1941) link_ALPHA1-2 : bond 0.00395 ( 3) link_ALPHA1-2 : angle 1.51122 ( 9) link_ALPHA1-3 : bond 0.00736 ( 9) link_ALPHA1-3 : angle 1.70598 ( 27) link_ALPHA1-6 : bond 0.00630 ( 6) link_ALPHA1-6 : angle 1.83068 ( 18) link_BETA1-4 : bond 0.00518 ( 33) link_BETA1-4 : angle 1.79190 ( 99) link_NAG-ASN : bond 0.00600 ( 48) link_NAG-ASN : angle 3.14502 ( 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 423 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 369 time to evaluate : 0.972 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 617 LYS cc_start: 0.8477 (mttm) cc_final: 0.7966 (mtpt) REVERT: D 51 MET cc_start: 0.7958 (tmm) cc_final: 0.7682 (tmm) REVERT: G 164 GLU cc_start: 0.6746 (mp0) cc_final: 0.6386 (mp0) REVERT: G 211 ASP cc_start: 0.8005 (t0) cc_final: 0.7798 (t70) REVERT: H 29 MET cc_start: 0.3874 (mmt) cc_final: 0.2938 (tmm) REVERT: H 100 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7187 (ttp80) REVERT: A 535 MET cc_start: 0.6877 (ttt) cc_final: 0.6671 (ttm) REVERT: A 544 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 638 TYR cc_start: 0.6429 (p90) cc_final: 0.6172 (p90) REVERT: F 61 SER cc_start: 0.6660 (m) cc_final: 0.6455 (m) REVERT: I 164 GLU cc_start: 0.6629 (mp0) cc_final: 0.5791 (mp0) REVERT: J 100 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7323 (ttp80) REVERT: K 36 TYR cc_start: 0.7018 (m-10) cc_final: 0.6815 (m-10) REVERT: M 583 ILE cc_start: 0.9002 (mm) cc_final: 0.8660 (mt) REVERT: P 164 GLU cc_start: 0.6730 (mp0) cc_final: 0.6017 (mp0) outliers start: 54 outliers final: 50 residues processed: 405 average time/residue: 0.2007 time to fit residues: 121.8256 Evaluate side-chains 410 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 359 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 85 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 242 VAL 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 497 LYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 84 CYS 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 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 447 ILE Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 588 LYS Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 68 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 323 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 260 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 205 optimal weight: 0.0060 chunk 224 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN A 543 GLN F 34 GLN ** N 57 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 = 0.4290 r_free = 0.4290 target = 0.200328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162276 restraints weight = 33711.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162877 restraints weight = 33099.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164516 restraints weight = 30620.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164573 restraints weight = 23003.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164983 restraints weight = 20476.191| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26067 Z= 0.106 Angle : 0.619 16.420 35589 Z= 0.292 Chirality : 0.047 0.720 4185 Planarity : 0.004 0.046 4353 Dihedral : 8.529 72.518 5343 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.46 % Favored : 95.17 % Rotamer: Outliers : 1.92 % Allowed : 18.38 % Favored : 79.70 % 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: -0.90 (0.15), residues: 3003 helix: 0.98 (0.28), residues: 375 sheet: -0.40 (0.17), residues: 939 loop : -1.07 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 542 TYR 0.016 0.001 TYR I 173 PHE 0.015 0.001 PHE D 64 TRP 0.044 0.001 TRP G 35 HIS 0.004 0.001 HIS K 92 Details of bonding type rmsd covalent geometry : bond 0.00233 (25926) covalent geometry : angle 0.57778 (35208) SS BOND : bond 0.00274 ( 42) SS BOND : angle 0.73074 ( 84) hydrogen bonds : bond 0.02961 ( 705) hydrogen bonds : angle 4.95145 ( 1941) link_ALPHA1-2 : bond 0.00415 ( 3) link_ALPHA1-2 : angle 1.47486 ( 9) link_ALPHA1-3 : bond 0.00744 ( 9) link_ALPHA1-3 : angle 1.70252 ( 27) link_ALPHA1-6 : bond 0.00676 ( 6) link_ALPHA1-6 : angle 1.76086 ( 18) link_BETA1-4 : bond 0.00536 ( 33) link_BETA1-4 : angle 1.79860 ( 99) link_NAG-ASN : bond 0.00594 ( 48) link_NAG-ASN : angle 3.07795 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.21 seconds wall clock time: 73 minutes 9.08 seconds (4389.08 seconds total)