Starting phenix.real_space_refine on Thu Mar 5 23:31:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.map" model { file = "/net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uov_26655/03_2026/7uov_26655.cif" } resolution = 2.75 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7914 atoms to isotropic. 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 117 5.16 5 C 12394 2.51 5 N 3155 2.21 5 O 4091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19757 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "a" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "b" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "F" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "c" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "R" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "Q" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.31, per 1000 atoms: 0.22 Number of scatterers: 19757 At special positions: 0 Unit cell: (145.86, 147.84, 112.86, 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 117 16.00 O 4091 8.00 N 3155 7.00 C 12394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 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 J 4 " - " MAN J 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " " MAN j 4 " - " MAN j 5 " " MAN p 4 " - " MAN p 5 " " MAN u 4 " - " MAN u 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 4 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 6 " " BMA j 3 " - " MAN j 6 " " BMA m 3 " - " MAN m 5 " " BMA p 3 " - " MAN p 6 " " BMA u 3 " - " MAN u 6 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " 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 s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " BETA1-6 " NAG K 1 " - " FUC K 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 4 " " NAG X 1 " - " FUC X 4 " " NAG Y 1 " - " FUC Y 6 " " NAG d 1 " - " FUC d 4 " " NAG e 1 " - " FUC e 4 " " NAG l 1 " - " FUC l 4 " " NAG m 1 " - " FUC m 6 " " NAG n 1 " - " FUC n 5 " " NAG r 1 " - " FUC r 4 " " NAG w 1 " - " FUC w 4 " " NAG x 1 " - " FUC x 6 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG I 1 " - " ASN A 79 " " NAG J 1 " - " ASN A 89 " " NAG K 1 " - " ASN A 109 " " NAG M 1 " - " ASN A 119 " " NAG N 1 " - " ASN A 167 " " NAG U 1 " - " ASN A 224 " " NAG V 1 " - " ASN a 365 " " NAG W 1 " - " ASN a 373 " " NAG X 1 " - " ASN a 390 " " NAG Y 1 " - " ASN a 395 " " NAG Z 1 " - " ASN B 89 " " NAG d 1 " - " ASN B 109 " " NAG e 1 " - " ASN B 119 " " NAG f 1 " - " ASN B 167 " " NAG g 1 " - " ASN B 79 " " NAG h 1 " - " ASN B 99 " " NAG i 1 " - " ASN B 224 " " NAG j 1 " - " ASN b 365 " " NAG k 1 " - " ASN b 373 " " NAG l 1 " - " ASN b 390 " " NAG m 1 " - " ASN b 395 " " NAG n 1 " - " ASN C 109 " " NAG o 1 " - " ASN C 79 " " NAG p 1 " - " ASN C 89 " " NAG q 1 " - " ASN C 99 " " NAG r 1 " - " ASN C 119 " " NAG s 1 " - " ASN C 167 " " NAG t 1 " - " ASN C 224 " " NAG u 1 " - " ASN c 365 " " NAG v 1 " - " ASN c 373 " " NAG w 1 " - " ASN c 390 " " NAG x 1 " - " ASN c 395 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 670.4 milliseconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 44 sheets defined 21.1% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.007A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.505A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.068A pdb=" N LYS A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.507A pdb=" N LEU A 203 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 333 through 341 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.825A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 416 removed outlier: 3.506A pdb=" N GLN a 416 " --> pdb=" O THR a 412 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.736A pdb=" N PHE T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.990A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.799A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.566A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.768A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.590A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.865A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.070A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.728A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 340 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.885A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 416 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.902A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.696A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.801A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.942A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 340 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.834A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 416 removed outlier: 3.792A pdb=" N GLN c 416 " --> pdb=" O THR c 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 4.012A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 23 removed outlier: 3.653A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.250A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG H 97 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.622A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.622A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA9, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB1, first strand: chain 'T' and resid 10 through 11 removed outlier: 6.555A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 10 through 11 removed outlier: 3.720A pdb=" N SER T 97 " --> pdb=" O GLN T 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 19 through 29 removed outlier: 6.090A pdb=" N THR T 69 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.612A pdb=" N VAL S 5 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 57 through 60 removed outlier: 6.560A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS S 96 " --> pdb=" O TRP S 118 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP S 118 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 98 " --> pdb=" O ASP S 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 57 through 60 removed outlier: 6.560A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.509A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR D 99 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D 111 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.108A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.076A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.730A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.867A pdb=" N SER P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'O' and resid 57 through 60 removed outlier: 6.801A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL O 117 " --> pdb=" O ARG O 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 57 through 60 removed outlier: 6.801A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 57 through 58 removed outlier: 5.814A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TRP F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG F 97 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 108 " --> pdb=" O TYR F 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.632A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AE1, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AE2, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AE3, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.471A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.723A pdb=" N SER R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS Q 96 " --> pdb=" O TRP Q 118 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP Q 118 " --> pdb=" O CYS Q 96 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG Q 98 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5923 1.34 - 1.46: 5348 1.46 - 1.58: 8750 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 20195 Sorted by residual: bond pdb=" C1 NAG w 1 " pdb=" O5 NAG w 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C3 BMA x 3 " pdb=" O3 BMA x 3 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C5 MAN n 4 " pdb=" O5 MAN n 4 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C3 BMA m 3 " pdb=" O3 BMA m 3 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 20190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 26260 1.75 - 3.50: 824 3.50 - 5.25: 250 5.25 - 7.00: 81 7.00 - 8.75: 7 Bond angle restraints: 27422 Sorted by residual: angle pdb=" C PHE S 54 " pdb=" N ASN S 55 " pdb=" CA ASN S 55 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C PHE O 54 " pdb=" N ASN O 55 " pdb=" CA ASN O 55 " ideal model delta sigma weight residual 125.66 133.60 -7.94 1.85e+00 2.92e-01 1.84e+01 angle pdb=" C LEU c 394 " pdb=" N ASN c 395 " pdb=" CA ASN c 395 " ideal model delta sigma weight residual 122.74 116.60 6.14 1.82e+00 3.02e-01 1.14e+01 angle pdb=" C ILE T 30 " pdb=" N ASN T 31 " pdb=" CA ASN T 31 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.64e+00 angle pdb=" C ASN A 119 " pdb=" CA ASN A 119 " pdb=" CB ASN A 119 " ideal model delta sigma weight residual 110.81 115.92 -5.11 1.65e+00 3.67e-01 9.61e+00 ... (remaining 27417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 12416 24.14 - 48.28: 673 48.28 - 72.42: 125 72.42 - 96.56: 160 96.56 - 120.70: 104 Dihedral angle restraints: 13478 sinusoidal: 6809 harmonic: 6669 Sorted by residual: dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -171.68 85.68 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS c 364 " pdb=" SG CYS c 364 " pdb=" SG CYS c 385 " pdb=" CB CYS c 385 " ideal model delta sinusoidal sigma weight residual -86.00 -168.53 82.53 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS b 364 " pdb=" SG CYS b 364 " pdb=" SG CYS b 385 " pdb=" CB CYS b 385 " ideal model delta sinusoidal sigma weight residual -86.00 -164.39 78.39 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3271 0.117 - 0.234: 103 0.234 - 0.351: 27 0.351 - 0.468: 1 0.468 - 0.585: 2 Chirality restraints: 3404 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN b 365 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C1 NAG x 1 " pdb=" ND2 ASN c 395 " pdb=" C2 NAG x 1 " pdb=" O5 NAG x 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 3401 not shown) Planarity restraints: 3293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 105 " -0.044 2.00e-02 2.50e+03 3.63e-02 3.29e+01 pdb=" CG TRP F 105 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP F 105 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP F 105 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 105 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 105 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 105 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 105 " -0.041 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP H 105 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP H 105 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 105 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 105 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.037 2.00e-02 2.50e+03 3.49e-02 1.52e+01 pdb=" CG ASN C 109 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG n 1 " 0.036 2.00e-02 2.50e+03 ... (remaining 3290 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 756 2.72 - 3.26: 18875 3.26 - 3.81: 31371 3.81 - 4.35: 39525 4.35 - 4.90: 68063 Nonbonded interactions: 158590 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb=" OH TYR G 86 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN c 395 " pdb=" N2 NAG x 1 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASN C 167 " pdb=" OG SER C 169 " model vdw 2.237 3.040 nonbonded pdb=" O GLY Q 66 " pdb=" NH1 ARG Q 84 " model vdw 2.240 3.120 nonbonded pdb=" NZ LYS A 116 " pdb=" O7 NAG N 1 " model vdw 2.254 3.120 ... (remaining 158585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 59 through 259) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'f' selection = chain 'g' selection = chain 'o' selection = chain 's' } ncs_group { reference = (chain 'J' and resid 1 through 5) selection = (chain 'V' and resid 1 through 5) selection = (chain 'Y' and resid 1 through 5) selection = (chain 'Z' and resid 1 through 5) selection = (chain 'j' and resid 1 through 5) selection = (chain 'm' and resid 1 through 5) selection = (chain 'p' and resid 1 through 5) selection = (chain 'u' and resid 1 through 5) selection = (chain 'x' and resid 1 through 5) } ncs_group { reference = chain 'K' selection = chain 'n' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'd' selection = chain 'e' selection = chain 'l' selection = chain 'r' selection = chain 'w' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'q' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.870 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 0.073 20352 Z= 0.242 Angle : 0.905 19.256 27863 Z= 0.375 Chirality : 0.054 0.585 3404 Planarity : 0.004 0.057 3260 Dihedral : 20.504 120.698 9122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2250 helix: 0.82 (0.29), residues: 351 sheet: 0.84 (0.20), residues: 669 loop : -0.50 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 103 TYR 0.012 0.001 TYR F 101 PHE 0.013 0.001 PHE b 399 TRP 0.096 0.002 TRP F 105 HIS 0.008 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00493 (20195) covalent geometry : angle 0.81763 (27422) SS BOND : bond 0.00338 ( 30) SS BOND : angle 0.96739 ( 60) hydrogen bonds : bond 0.14886 ( 714) hydrogen bonds : angle 5.98716 ( 1944) link_ALPHA1-2 : bond 0.00472 ( 6) link_ALPHA1-2 : angle 2.01492 ( 18) link_ALPHA1-3 : bond 0.00865 ( 11) link_ALPHA1-3 : angle 2.87288 ( 33) link_ALPHA1-6 : bond 0.00457 ( 9) link_ALPHA1-6 : angle 1.61679 ( 27) link_BETA1-4 : bond 0.00947 ( 56) link_BETA1-4 : angle 2.47074 ( 168) link_BETA1-6 : bond 0.00457 ( 12) link_BETA1-6 : angle 1.73183 ( 36) link_NAG-ASN : bond 0.01115 ( 33) link_NAG-ASN : angle 5.40858 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: L 83 PHE cc_start: 0.6594 (m-80) cc_final: 0.6382 (m-80) REVERT: D 38 ARG cc_start: 0.7856 (ttp-170) cc_final: 0.7511 (ttp-170) REVERT: E 27 GLN cc_start: 0.8821 (pm20) cc_final: 0.8470 (pm20) REVERT: E 97 THR cc_start: 0.8576 (m) cc_final: 0.8365 (t) REVERT: P 79 GLN cc_start: 0.7734 (mt0) cc_final: 0.7483 (mm110) REVERT: Q 13 LYS cc_start: 0.8872 (pptt) cc_final: 0.8595 (ttpt) outliers start: 0 outliers final: 2 residues processed: 429 average time/residue: 0.7530 time to fit residues: 355.0172 Evaluate side-chains 354 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 411 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN H 107 ASN D 76 ASN B 127 ASN B 146 ASN P 31 ASN F 76 ASN C 230 HIS c 406 GLN c 409 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072569 restraints weight = 41473.335| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.50 r_work: 0.2961 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20352 Z= 0.151 Angle : 0.784 16.775 27863 Z= 0.347 Chirality : 0.046 0.523 3404 Planarity : 0.004 0.053 3260 Dihedral : 16.707 117.830 5028 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.26 % Allowed : 12.17 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2250 helix: 0.87 (0.28), residues: 384 sheet: 0.90 (0.20), residues: 681 loop : -0.52 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 24 TYR 0.019 0.001 TYR R 49 PHE 0.014 0.001 PHE G 83 TRP 0.034 0.001 TRP F 105 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00335 (20195) covalent geometry : angle 0.69647 (27422) SS BOND : bond 0.00371 ( 30) SS BOND : angle 1.14792 ( 60) hydrogen bonds : bond 0.03912 ( 714) hydrogen bonds : angle 4.79540 ( 1944) link_ALPHA1-2 : bond 0.00757 ( 6) link_ALPHA1-2 : angle 2.28563 ( 18) link_ALPHA1-3 : bond 0.01367 ( 11) link_ALPHA1-3 : angle 3.38616 ( 33) link_ALPHA1-6 : bond 0.00700 ( 9) link_ALPHA1-6 : angle 2.08767 ( 27) link_BETA1-4 : bond 0.00610 ( 56) link_BETA1-4 : angle 2.34933 ( 168) link_BETA1-6 : bond 0.00579 ( 12) link_BETA1-6 : angle 1.67432 ( 36) link_NAG-ASN : bond 0.00904 ( 33) link_NAG-ASN : angle 4.61207 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 382 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.6793 (t0) cc_final: 0.6567 (t0) REVERT: L 36 TYR cc_start: 0.7446 (m-80) cc_final: 0.7182 (m-80) REVERT: L 45 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8135 (ptt180) REVERT: L 79 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6594 (mm-30) REVERT: T 42 GLN cc_start: 0.6652 (mp10) cc_final: 0.6425 (mp10) REVERT: S 73 ASP cc_start: 0.7707 (t0) cc_final: 0.7362 (t70) REVERT: D 38 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7935 (ttp-170) REVERT: E 17 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7524 (mp0) REVERT: E 27 GLN cc_start: 0.8666 (pm20) cc_final: 0.8088 (pm20) REVERT: E 97 THR cc_start: 0.7974 (m) cc_final: 0.7443 (t) REVERT: b 287 GLU cc_start: 0.8673 (mp0) cc_final: 0.8204 (mp0) REVERT: P 39 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7196 (mppt) REVERT: P 78 MET cc_start: 0.7945 (ttt) cc_final: 0.7353 (tmm) REVERT: P 79 GLN cc_start: 0.6258 (mt0) cc_final: 0.6024 (mm110) REVERT: O 3 GLN cc_start: 0.8571 (pm20) cc_final: 0.8356 (pm20) REVERT: O 82 GLU cc_start: 0.8564 (pt0) cc_final: 0.8249 (pt0) REVERT: O 84 ARG cc_start: 0.8118 (mpt90) cc_final: 0.7911 (mmt-90) REVERT: F 72 ASP cc_start: 0.8124 (t0) cc_final: 0.7846 (t0) REVERT: G 17 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8420 (tm-30) REVERT: Q 65 GLN cc_start: 0.8548 (mt0) cc_final: 0.8130 (mp10) outliers start: 25 outliers final: 10 residues processed: 393 average time/residue: 0.7453 time to fit residues: 322.0252 Evaluate side-chains 369 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 357 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 134 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN T 89 GLN B 146 ASN b 295 ASN P 31 ASN O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.069345 restraints weight = 41884.771| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.51 r_work: 0.2893 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20352 Z= 0.197 Angle : 0.795 15.800 27863 Z= 0.356 Chirality : 0.047 0.503 3404 Planarity : 0.004 0.056 3260 Dihedral : 14.028 119.628 5024 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.61 % Allowed : 15.54 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2250 helix: 0.92 (0.28), residues: 384 sheet: 0.89 (0.20), residues: 681 loop : -0.57 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 24 TYR 0.021 0.001 TYR G 86 PHE 0.014 0.001 PHE b 399 TRP 0.027 0.002 TRP b 386 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00455 (20195) covalent geometry : angle 0.71672 (27422) SS BOND : bond 0.00513 ( 30) SS BOND : angle 1.38254 ( 60) hydrogen bonds : bond 0.04088 ( 714) hydrogen bonds : angle 4.69973 ( 1944) link_ALPHA1-2 : bond 0.00625 ( 6) link_ALPHA1-2 : angle 2.45630 ( 18) link_ALPHA1-3 : bond 0.01247 ( 11) link_ALPHA1-3 : angle 3.16471 ( 33) link_ALPHA1-6 : bond 0.00556 ( 9) link_ALPHA1-6 : angle 1.99868 ( 27) link_BETA1-4 : bond 0.00463 ( 56) link_BETA1-4 : angle 2.30669 ( 168) link_BETA1-6 : bond 0.00462 ( 12) link_BETA1-6 : angle 1.74766 ( 36) link_NAG-ASN : bond 0.00735 ( 33) link_NAG-ASN : angle 4.34407 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7045 (t0) cc_final: 0.6755 (t0) REVERT: L 36 TYR cc_start: 0.7661 (m-80) cc_final: 0.7412 (m-80) REVERT: a 404 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7770 (mp0) REVERT: T 42 GLN cc_start: 0.6583 (mp10) cc_final: 0.6178 (mp10) REVERT: S 73 ASP cc_start: 0.7684 (t0) cc_final: 0.7254 (t70) REVERT: S 82 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6757 (tm-30) REVERT: D 72 ASP cc_start: 0.7921 (t0) cc_final: 0.7656 (t0) REVERT: D 97 ARG cc_start: 0.7690 (ttt180) cc_final: 0.7271 (ttt-90) REVERT: E 27 GLN cc_start: 0.8700 (pm20) cc_final: 0.8096 (pm20) REVERT: E 45 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7482 (ptt90) REVERT: B 116 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: B 130 ASP cc_start: 0.8640 (t0) cc_final: 0.8318 (t0) REVERT: b 286 ILE cc_start: 0.8569 (pt) cc_final: 0.8333 (pp) REVERT: b 287 GLU cc_start: 0.8645 (mp0) cc_final: 0.8435 (mp0) REVERT: P 39 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7203 (mppt) REVERT: P 78 MET cc_start: 0.8207 (ttt) cc_final: 0.7590 (tmm) REVERT: P 79 GLN cc_start: 0.6696 (mt0) cc_final: 0.6302 (mm110) REVERT: P 100 GLN cc_start: 0.7950 (mp10) cc_final: 0.7583 (pm20) REVERT: F 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7844 (t0) REVERT: G 17 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8466 (tm-30) REVERT: C 100 GLU cc_start: 0.8688 (mm-30) cc_final: 0.7997 (pm20) REVERT: R 24 ARG cc_start: 0.8289 (ttm110) cc_final: 0.8048 (ttm110) REVERT: R 103 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7831 (ttm-80) REVERT: Q 65 GLN cc_start: 0.8507 (mt0) cc_final: 0.8151 (mt0) outliers start: 52 outliers final: 22 residues processed: 395 average time/residue: 0.7677 time to fit residues: 333.0823 Evaluate side-chains 375 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 350 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 118 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 165 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN b 295 ASN P 31 ASN O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069989 restraints weight = 41718.285| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.52 r_work: 0.2905 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20352 Z= 0.156 Angle : 0.761 14.956 27863 Z= 0.340 Chirality : 0.045 0.507 3404 Planarity : 0.004 0.050 3260 Dihedral : 12.508 119.044 5024 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 17.04 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2250 helix: 0.97 (0.28), residues: 384 sheet: 0.83 (0.20), residues: 696 loop : -0.59 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 24 TYR 0.013 0.001 TYR R 49 PHE 0.016 0.001 PHE G 83 TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00355 (20195) covalent geometry : angle 0.68726 (27422) SS BOND : bond 0.00374 ( 30) SS BOND : angle 1.16201 ( 60) hydrogen bonds : bond 0.03549 ( 714) hydrogen bonds : angle 4.59028 ( 1944) link_ALPHA1-2 : bond 0.00695 ( 6) link_ALPHA1-2 : angle 2.38990 ( 18) link_ALPHA1-3 : bond 0.01339 ( 11) link_ALPHA1-3 : angle 3.20168 ( 33) link_ALPHA1-6 : bond 0.00659 ( 9) link_ALPHA1-6 : angle 1.97022 ( 27) link_BETA1-4 : bond 0.00493 ( 56) link_BETA1-4 : angle 2.16734 ( 168) link_BETA1-6 : bond 0.00545 ( 12) link_BETA1-6 : angle 1.72458 ( 36) link_NAG-ASN : bond 0.00791 ( 33) link_NAG-ASN : angle 4.07225 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 376 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7060 (t0) cc_final: 0.6751 (t0) REVERT: L 36 TYR cc_start: 0.7649 (m-80) cc_final: 0.7371 (m-80) REVERT: L 100 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8287 (mp10) REVERT: a 404 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7712 (mp0) REVERT: T 42 GLN cc_start: 0.6618 (mp10) cc_final: 0.6103 (mp10) REVERT: S 73 ASP cc_start: 0.7666 (t0) cc_final: 0.7225 (t70) REVERT: S 82 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6732 (tm-30) REVERT: D 46 GLU cc_start: 0.7088 (pt0) cc_final: 0.6523 (pm20) REVERT: E 17 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7733 (mp0) REVERT: E 27 GLN cc_start: 0.8706 (pm20) cc_final: 0.8092 (pm20) REVERT: E 45 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7479 (ptt90) REVERT: B 130 ASP cc_start: 0.8675 (t0) cc_final: 0.8343 (t0) REVERT: b 286 ILE cc_start: 0.8579 (pt) cc_final: 0.8357 (pp) REVERT: b 287 GLU cc_start: 0.8684 (mp0) cc_final: 0.8403 (mp0) REVERT: b 410 MET cc_start: 0.8808 (mmm) cc_final: 0.8581 (mtm) REVERT: P 78 MET cc_start: 0.8130 (ttt) cc_final: 0.7685 (tmm) REVERT: P 79 GLN cc_start: 0.6433 (mt0) cc_final: 0.6038 (mm110) REVERT: P 81 GLU cc_start: 0.8129 (pm20) cc_final: 0.7878 (pp20) REVERT: P 100 GLN cc_start: 0.8046 (mp10) cc_final: 0.7635 (pm20) REVERT: O 3 GLN cc_start: 0.8538 (pm20) cc_final: 0.8303 (pm20) REVERT: O 13 LYS cc_start: 0.8645 (tppt) cc_final: 0.8317 (tptt) REVERT: O 82 GLU cc_start: 0.8563 (pt0) cc_final: 0.8135 (pt0) REVERT: F 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7919 (t0) REVERT: G 17 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8465 (tm-30) REVERT: C 75 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: C 100 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8028 (pm20) REVERT: c 396 GLU cc_start: 0.9025 (mp0) cc_final: 0.8786 (mp0) REVERT: R 103 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7840 (ttm-80) REVERT: Q 65 GLN cc_start: 0.8472 (mt0) cc_final: 0.8083 (mt0) outliers start: 63 outliers final: 28 residues processed: 416 average time/residue: 0.7515 time to fit residues: 344.1851 Evaluate side-chains 385 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 174 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.0010 chunk 146 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN D 76 ASN b 295 ASN P 31 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.071492 restraints weight = 41436.847| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.49 r_work: 0.2934 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20352 Z= 0.129 Angle : 0.735 13.785 27863 Z= 0.330 Chirality : 0.044 0.493 3404 Planarity : 0.004 0.064 3260 Dihedral : 11.519 118.579 5024 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.92 % Allowed : 18.75 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2250 helix: 1.08 (0.28), residues: 384 sheet: 0.81 (0.20), residues: 696 loop : -0.56 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 24 TYR 0.024 0.001 TYR R 49 PHE 0.012 0.001 PHE D 78 TRP 0.011 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00284 (20195) covalent geometry : angle 0.67016 (27422) SS BOND : bond 0.00343 ( 30) SS BOND : angle 1.00196 ( 60) hydrogen bonds : bond 0.03219 ( 714) hydrogen bonds : angle 4.47040 ( 1944) link_ALPHA1-2 : bond 0.00778 ( 6) link_ALPHA1-2 : angle 2.36955 ( 18) link_ALPHA1-3 : bond 0.01371 ( 11) link_ALPHA1-3 : angle 3.14210 ( 33) link_ALPHA1-6 : bond 0.00715 ( 9) link_ALPHA1-6 : angle 1.96586 ( 27) link_BETA1-4 : bond 0.00515 ( 56) link_BETA1-4 : angle 1.98370 ( 168) link_BETA1-6 : bond 0.00645 ( 12) link_BETA1-6 : angle 1.59858 ( 36) link_NAG-ASN : bond 0.00816 ( 33) link_NAG-ASN : angle 3.76454 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 366 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7050 (t0) cc_final: 0.6729 (t0) REVERT: L 36 TYR cc_start: 0.7602 (m-80) cc_final: 0.6847 (m-80) REVERT: L 89 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: L 100 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8298 (mp10) REVERT: L 105 GLU cc_start: 0.7479 (mp0) cc_final: 0.7219 (pm20) REVERT: a 404 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7689 (mp0) REVERT: T 42 GLN cc_start: 0.6665 (mp10) cc_final: 0.6086 (mp10) REVERT: S 73 ASP cc_start: 0.7672 (t0) cc_final: 0.7211 (t0) REVERT: S 82 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6721 (tm-30) REVERT: D 38 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7281 (ttp-170) REVERT: D 46 GLU cc_start: 0.7147 (pt0) cc_final: 0.6657 (pm20) REVERT: E 17 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7682 (mp0) REVERT: E 27 GLN cc_start: 0.8714 (pm20) cc_final: 0.8097 (pm20) REVERT: E 45 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7518 (ptt90) REVERT: B 130 ASP cc_start: 0.8701 (t0) cc_final: 0.8379 (t0) REVERT: b 286 ILE cc_start: 0.8601 (pt) cc_final: 0.8306 (pp) REVERT: b 287 GLU cc_start: 0.8660 (mp0) cc_final: 0.8045 (mp0) REVERT: P 78 MET cc_start: 0.8137 (ttt) cc_final: 0.7649 (tmm) REVERT: P 100 GLN cc_start: 0.8071 (mp10) cc_final: 0.7644 (pm20) REVERT: O 3 GLN cc_start: 0.8597 (pm20) cc_final: 0.8343 (pm20) REVERT: O 13 LYS cc_start: 0.8687 (tppt) cc_final: 0.8394 (tptt) REVERT: O 82 GLU cc_start: 0.8454 (pt0) cc_final: 0.8072 (pt0) REVERT: F 45 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7376 (pp) REVERT: F 72 ASP cc_start: 0.8264 (t0) cc_final: 0.7942 (t0) REVERT: G 17 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8505 (tm-30) REVERT: C 75 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.6995 (mmt) REVERT: C 100 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8042 (pm20) REVERT: c 396 GLU cc_start: 0.9028 (mp0) cc_final: 0.8764 (mp0) REVERT: R 24 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7780 (ttm110) REVERT: R 70 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7083 (mm-30) REVERT: R 100 GLN cc_start: 0.8672 (mm110) cc_final: 0.8289 (mp10) REVERT: R 103 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7833 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8746 (tp40) cc_final: 0.8507 (tp40) REVERT: Q 65 GLN cc_start: 0.8481 (mt0) cc_final: 0.8241 (mt0) outliers start: 58 outliers final: 23 residues processed: 402 average time/residue: 0.7562 time to fit residues: 334.7078 Evaluate side-chains 384 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 356 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 214 optimal weight: 7.9990 chunk 204 optimal weight: 0.0470 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN D 77 GLN P 31 ASN O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070092 restraints weight = 41723.460| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.49 r_work: 0.2910 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20352 Z= 0.171 Angle : 0.760 13.664 27863 Z= 0.345 Chirality : 0.045 0.497 3404 Planarity : 0.004 0.064 3260 Dihedral : 11.109 118.222 5024 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.42 % Allowed : 19.46 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2250 helix: 1.02 (0.28), residues: 384 sheet: 0.82 (0.20), residues: 696 loop : -0.63 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 24 TYR 0.025 0.001 TYR R 49 PHE 0.018 0.001 PHE G 83 TRP 0.011 0.001 TRP F 47 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00396 (20195) covalent geometry : angle 0.69355 (27422) SS BOND : bond 0.00366 ( 30) SS BOND : angle 1.25417 ( 60) hydrogen bonds : bond 0.03516 ( 714) hydrogen bonds : angle 4.50290 ( 1944) link_ALPHA1-2 : bond 0.00673 ( 6) link_ALPHA1-2 : angle 2.45557 ( 18) link_ALPHA1-3 : bond 0.01273 ( 11) link_ALPHA1-3 : angle 3.19036 ( 33) link_ALPHA1-6 : bond 0.00659 ( 9) link_ALPHA1-6 : angle 2.03829 ( 27) link_BETA1-4 : bond 0.00457 ( 56) link_BETA1-4 : angle 1.97647 ( 168) link_BETA1-6 : bond 0.00512 ( 12) link_BETA1-6 : angle 1.69982 ( 36) link_NAG-ASN : bond 0.00804 ( 33) link_NAG-ASN : angle 3.85965 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7111 (t0) cc_final: 0.6786 (t0) REVERT: L 36 TYR cc_start: 0.7687 (m-80) cc_final: 0.6970 (m-80) REVERT: L 89 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: L 103 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: a 404 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7681 (mp0) REVERT: T 42 GLN cc_start: 0.6653 (mp10) cc_final: 0.5992 (mp10) REVERT: T 82 ASP cc_start: 0.8316 (m-30) cc_final: 0.8068 (m-30) REVERT: S 73 ASP cc_start: 0.7682 (t0) cc_final: 0.7218 (t0) REVERT: S 82 GLU cc_start: 0.7698 (tm-30) cc_final: 0.6634 (tm-30) REVERT: D 38 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7703 (ptm160) REVERT: D 72 ASP cc_start: 0.7875 (t0) cc_final: 0.7490 (t0) REVERT: D 75 LYS cc_start: 0.9266 (pttt) cc_final: 0.8967 (pmmt) REVERT: E 17 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7691 (mp0) REVERT: E 27 GLN cc_start: 0.8726 (pm20) cc_final: 0.8093 (pm20) REVERT: E 45 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7510 (ptt90) REVERT: B 130 ASP cc_start: 0.8725 (t0) cc_final: 0.8402 (t0) REVERT: b 286 ILE cc_start: 0.8617 (pt) cc_final: 0.8366 (pp) REVERT: b 287 GLU cc_start: 0.8662 (mp0) cc_final: 0.8399 (mp0) REVERT: P 24 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7913 (ttm110) REVERT: P 39 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7179 (mppt) REVERT: P 78 MET cc_start: 0.8249 (ttt) cc_final: 0.7716 (tmm) REVERT: P 81 GLU cc_start: 0.8186 (pm20) cc_final: 0.7968 (pm20) REVERT: P 82 ASP cc_start: 0.7154 (m-30) cc_final: 0.6633 (m-30) REVERT: P 100 GLN cc_start: 0.8120 (mp10) cc_final: 0.7666 (pm20) REVERT: O 3 GLN cc_start: 0.8616 (pm20) cc_final: 0.8357 (pm20) REVERT: O 13 LYS cc_start: 0.8735 (tppt) cc_final: 0.8521 (tptt) REVERT: O 73 ASP cc_start: 0.6634 (t0) cc_final: 0.6424 (t70) REVERT: O 82 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: F 45 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7372 (pp) REVERT: F 72 ASP cc_start: 0.8241 (t0) cc_final: 0.7940 (t0) REVERT: G 17 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8454 (tm-30) REVERT: C 100 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8043 (pm20) REVERT: c 396 GLU cc_start: 0.8966 (mp0) cc_final: 0.8675 (mp0) REVERT: R 100 GLN cc_start: 0.8687 (mm110) cc_final: 0.8274 (mp10) REVERT: R 103 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7845 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8780 (tp40) cc_final: 0.8552 (tp40) REVERT: Q 65 GLN cc_start: 0.8508 (mt0) cc_final: 0.8213 (mt0) outliers start: 68 outliers final: 31 residues processed: 408 average time/residue: 0.7574 time to fit residues: 340.2685 Evaluate side-chains 391 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 69 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN D 77 GLN ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067831 restraints weight = 41917.042| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.49 r_work: 0.2862 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20352 Z= 0.247 Angle : 0.832 13.402 27863 Z= 0.381 Chirality : 0.047 0.509 3404 Planarity : 0.004 0.070 3260 Dihedral : 11.086 118.168 5024 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.02 % Allowed : 19.61 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2250 helix: 0.84 (0.28), residues: 384 sheet: 0.71 (0.20), residues: 672 loop : -0.69 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 24 TYR 0.024 0.002 TYR R 49 PHE 0.017 0.002 PHE b 399 TRP 0.014 0.002 TRP F 47 HIS 0.006 0.001 HIS b 305 Details of bonding type rmsd covalent geometry : bond 0.00581 (20195) covalent geometry : angle 0.76734 (27422) SS BOND : bond 0.00457 ( 30) SS BOND : angle 1.66033 ( 60) hydrogen bonds : bond 0.04128 ( 714) hydrogen bonds : angle 4.67767 ( 1944) link_ALPHA1-2 : bond 0.00594 ( 6) link_ALPHA1-2 : angle 2.61418 ( 18) link_ALPHA1-3 : bond 0.01154 ( 11) link_ALPHA1-3 : angle 3.23728 ( 33) link_ALPHA1-6 : bond 0.00622 ( 9) link_ALPHA1-6 : angle 1.96298 ( 27) link_BETA1-4 : bond 0.00431 ( 56) link_BETA1-4 : angle 2.07725 ( 168) link_BETA1-6 : bond 0.00448 ( 12) link_BETA1-6 : angle 1.83660 ( 36) link_NAG-ASN : bond 0.00779 ( 33) link_NAG-ASN : angle 3.94791 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 364 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7147 (t0) cc_final: 0.6796 (t0) REVERT: L 13 LEU cc_start: 0.8585 (tp) cc_final: 0.8165 (tt) REVERT: L 36 TYR cc_start: 0.7912 (m-80) cc_final: 0.7595 (m-80) REVERT: L 100 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8207 (mp10) REVERT: L 105 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: a 350 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8407 (mt) REVERT: a 404 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7659 (mp0) REVERT: T 24 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8166 (ttp-110) REVERT: T 42 GLN cc_start: 0.6724 (mp10) cc_final: 0.6006 (mp10) REVERT: S 73 ASP cc_start: 0.7734 (t0) cc_final: 0.7256 (t0) REVERT: S 82 GLU cc_start: 0.7729 (tm-30) cc_final: 0.6685 (tm-30) REVERT: D 38 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7471 (ptm160) REVERT: E 27 GLN cc_start: 0.8759 (pm20) cc_final: 0.8128 (pm20) REVERT: E 45 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7433 (ptt90) REVERT: B 130 ASP cc_start: 0.8730 (t0) cc_final: 0.8390 (t0) REVERT: b 286 ILE cc_start: 0.8646 (pt) cc_final: 0.8419 (pp) REVERT: b 287 GLU cc_start: 0.8694 (mp0) cc_final: 0.8397 (mp0) REVERT: b 289 GLU cc_start: 0.8301 (pm20) cc_final: 0.8043 (tm-30) REVERT: P 39 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7253 (mppt) REVERT: P 78 MET cc_start: 0.8311 (ttt) cc_final: 0.7826 (tmm) REVERT: P 100 GLN cc_start: 0.8165 (mp10) cc_final: 0.7666 (pm20) REVERT: O 3 GLN cc_start: 0.8660 (pm20) cc_final: 0.8374 (pm20) REVERT: O 73 ASP cc_start: 0.6732 (t0) cc_final: 0.6504 (t70) REVERT: O 82 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: F 45 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7385 (pp) REVERT: F 72 ASP cc_start: 0.8264 (t0) cc_final: 0.7946 (t0) REVERT: G 17 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8518 (tm-30) REVERT: C 100 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8048 (pm20) REVERT: c 396 GLU cc_start: 0.8955 (mp0) cc_final: 0.8709 (mp0) REVERT: R 24 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8019 (ttm110) REVERT: R 103 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7886 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8842 (tp40) cc_final: 0.8639 (tp40) REVERT: Q 65 GLN cc_start: 0.8505 (mt0) cc_final: 0.8204 (mt0) outliers start: 80 outliers final: 39 residues processed: 413 average time/residue: 0.7305 time to fit residues: 332.6857 Evaluate side-chains 399 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 350 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 189 GLN a 409 ASN D 76 ASN D 77 GLN E 37 GLN b 295 ASN ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN c 409 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.069212 restraints weight = 41602.268| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.53 r_work: 0.2890 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20352 Z= 0.156 Angle : 0.779 13.510 27863 Z= 0.358 Chirality : 0.045 0.499 3404 Planarity : 0.004 0.076 3260 Dihedral : 10.599 117.586 5024 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.07 % Allowed : 21.37 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.18), residues: 2250 helix: 0.99 (0.28), residues: 384 sheet: 0.76 (0.20), residues: 660 loop : -0.64 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 24 TYR 0.022 0.001 TYR R 49 PHE 0.019 0.001 PHE G 83 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00357 (20195) covalent geometry : angle 0.71940 (27422) SS BOND : bond 0.00329 ( 30) SS BOND : angle 1.03605 ( 60) hydrogen bonds : bond 0.03512 ( 714) hydrogen bonds : angle 4.54621 ( 1944) link_ALPHA1-2 : bond 0.00707 ( 6) link_ALPHA1-2 : angle 2.51337 ( 18) link_ALPHA1-3 : bond 0.01309 ( 11) link_ALPHA1-3 : angle 3.15293 ( 33) link_ALPHA1-6 : bond 0.00799 ( 9) link_ALPHA1-6 : angle 1.85517 ( 27) link_BETA1-4 : bond 0.00483 ( 56) link_BETA1-4 : angle 1.92328 ( 168) link_BETA1-6 : bond 0.00519 ( 12) link_BETA1-6 : angle 1.66187 ( 36) link_NAG-ASN : bond 0.00904 ( 33) link_NAG-ASN : angle 3.73308 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7153 (t0) cc_final: 0.6800 (t0) REVERT: L 13 LEU cc_start: 0.8558 (tp) cc_final: 0.8195 (tt) REVERT: L 36 TYR cc_start: 0.7780 (m-80) cc_final: 0.7055 (m-80) REVERT: L 89 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: L 100 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8161 (mp10) REVERT: T 42 GLN cc_start: 0.6697 (mp10) cc_final: 0.6000 (mp10) REVERT: S 73 ASP cc_start: 0.7713 (t0) cc_final: 0.7230 (t0) REVERT: S 82 GLU cc_start: 0.7701 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 38 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7446 (ptm160) REVERT: D 43 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8421 (mtpp) REVERT: D 72 ASP cc_start: 0.7922 (t0) cc_final: 0.7583 (t0) REVERT: D 75 LYS cc_start: 0.9186 (pttt) cc_final: 0.8890 (pmmt) REVERT: E 17 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7851 (mp0) REVERT: E 27 GLN cc_start: 0.8745 (pm20) cc_final: 0.8116 (pm20) REVERT: E 45 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7452 (ptt90) REVERT: B 130 ASP cc_start: 0.8709 (t0) cc_final: 0.8354 (t0) REVERT: b 286 ILE cc_start: 0.8620 (pt) cc_final: 0.8407 (pp) REVERT: b 287 GLU cc_start: 0.8670 (mp0) cc_final: 0.8434 (mp0) REVERT: b 289 GLU cc_start: 0.8311 (pm20) cc_final: 0.8104 (tm-30) REVERT: P 24 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7936 (ttm110) REVERT: P 39 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7211 (mppt) REVERT: P 78 MET cc_start: 0.8232 (ttt) cc_final: 0.7724 (tmm) REVERT: P 81 GLU cc_start: 0.8100 (pm20) cc_final: 0.7833 (pm20) REVERT: P 82 ASP cc_start: 0.7156 (m-30) cc_final: 0.6678 (m-30) REVERT: P 100 GLN cc_start: 0.8184 (mp10) cc_final: 0.7688 (pm20) REVERT: O 3 GLN cc_start: 0.8719 (pm20) cc_final: 0.8420 (pm20) REVERT: O 73 ASP cc_start: 0.6720 (t0) cc_final: 0.6448 (t70) REVERT: F 45 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7268 (pp) REVERT: F 72 ASP cc_start: 0.8292 (t0) cc_final: 0.7978 (t0) REVERT: G 17 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8483 (tm-30) REVERT: C 100 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8041 (pm20) REVERT: c 396 GLU cc_start: 0.8911 (mp0) cc_final: 0.8592 (mp0) REVERT: R 103 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7869 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8803 (tp40) cc_final: 0.8536 (tp40) REVERT: Q 65 GLN cc_start: 0.8485 (mt0) cc_final: 0.8132 (mt0) outliers start: 61 outliers final: 35 residues processed: 406 average time/residue: 0.7627 time to fit residues: 340.6145 Evaluate side-chains 393 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 353 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 24 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 129 optimal weight: 0.0570 chunk 109 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN T 31 ASN O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070780 restraints weight = 41071.173| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.50 r_work: 0.2928 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20352 Z= 0.132 Angle : 0.763 13.405 27863 Z= 0.350 Chirality : 0.044 0.500 3404 Planarity : 0.004 0.082 3260 Dihedral : 10.076 116.728 5024 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.51 % Allowed : 22.02 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2250 helix: 1.09 (0.28), residues: 384 sheet: 0.84 (0.20), residues: 681 loop : -0.65 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 24 TYR 0.022 0.001 TYR R 49 PHE 0.011 0.001 PHE D 78 TRP 0.011 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00297 (20195) covalent geometry : angle 0.70998 (27422) SS BOND : bond 0.00295 ( 30) SS BOND : angle 0.85164 ( 60) hydrogen bonds : bond 0.03146 ( 714) hydrogen bonds : angle 4.41655 ( 1944) link_ALPHA1-2 : bond 0.00784 ( 6) link_ALPHA1-2 : angle 2.42927 ( 18) link_ALPHA1-3 : bond 0.01372 ( 11) link_ALPHA1-3 : angle 3.10650 ( 33) link_ALPHA1-6 : bond 0.00984 ( 9) link_ALPHA1-6 : angle 1.81035 ( 27) link_BETA1-4 : bond 0.00523 ( 56) link_BETA1-4 : angle 1.81501 ( 168) link_BETA1-6 : bond 0.00563 ( 12) link_BETA1-6 : angle 1.58530 ( 36) link_NAG-ASN : bond 0.00832 ( 33) link_NAG-ASN : angle 3.49583 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7094 (t0) cc_final: 0.6759 (t0) REVERT: L 13 LEU cc_start: 0.8586 (tp) cc_final: 0.8204 (tt) REVERT: L 36 TYR cc_start: 0.7618 (m-80) cc_final: 0.7379 (m-80) REVERT: L 61 ARG cc_start: 0.8006 (mpp80) cc_final: 0.7801 (mpp80) REVERT: L 100 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8141 (mp10) REVERT: T 4 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8068 (pp) REVERT: T 42 GLN cc_start: 0.6679 (mp10) cc_final: 0.6009 (mp10) REVERT: S 73 ASP cc_start: 0.7655 (t0) cc_final: 0.7173 (t0) REVERT: S 82 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6677 (tm-30) REVERT: D 38 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7564 (ptm160) REVERT: D 43 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8420 (mtpp) REVERT: D 72 ASP cc_start: 0.7901 (t0) cc_final: 0.7532 (t0) REVERT: D 75 LYS cc_start: 0.9127 (pttt) cc_final: 0.8844 (pmmt) REVERT: E 17 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8035 (mp0) REVERT: E 27 GLN cc_start: 0.8733 (pm20) cc_final: 0.8121 (pm20) REVERT: E 45 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: B 130 ASP cc_start: 0.8695 (t0) cc_final: 0.8363 (t0) REVERT: b 286 ILE cc_start: 0.8604 (pt) cc_final: 0.8376 (pp) REVERT: b 287 GLU cc_start: 0.8656 (mp0) cc_final: 0.8421 (mp0) REVERT: b 289 GLU cc_start: 0.8317 (pm20) cc_final: 0.8100 (tm-30) REVERT: P 24 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7950 (ttm110) REVERT: P 78 MET cc_start: 0.8191 (ttt) cc_final: 0.7622 (tmm) REVERT: P 100 GLN cc_start: 0.8197 (mp10) cc_final: 0.7701 (pm20) REVERT: O 3 GLN cc_start: 0.8728 (pm20) cc_final: 0.8424 (pm20) REVERT: O 73 ASP cc_start: 0.6640 (t0) cc_final: 0.6364 (t70) REVERT: F 45 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7231 (pp) REVERT: F 72 ASP cc_start: 0.8265 (t0) cc_final: 0.7963 (t0) REVERT: G 17 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8465 (tm-30) REVERT: C 100 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8038 (pm20) REVERT: c 396 GLU cc_start: 0.8927 (mp0) cc_final: 0.8665 (mp0) REVERT: R 100 GLN cc_start: 0.8638 (mm110) cc_final: 0.8239 (mp10) REVERT: R 103 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7812 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8811 (tp40) cc_final: 0.8584 (tp40) REVERT: Q 65 GLN cc_start: 0.8468 (mt0) cc_final: 0.8128 (mt0) outliers start: 50 outliers final: 26 residues processed: 400 average time/residue: 0.7551 time to fit residues: 332.2803 Evaluate side-chains 387 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 97 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 0.0470 chunk 43 optimal weight: 0.0040 chunk 200 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 409 ASN T 31 ASN D 76 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071732 restraints weight = 41271.186| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.49 r_work: 0.2940 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20352 Z= 0.130 Angle : 0.756 13.304 27863 Z= 0.347 Chirality : 0.043 0.493 3404 Planarity : 0.004 0.086 3260 Dihedral : 9.681 115.972 5024 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.06 % Allowed : 22.47 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2250 helix: 1.13 (0.29), residues: 384 sheet: 0.79 (0.20), residues: 678 loop : -0.57 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 24 TYR 0.030 0.001 TYR R 49 PHE 0.021 0.001 PHE G 83 TRP 0.014 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (20195) covalent geometry : angle 0.70446 (27422) SS BOND : bond 0.00296 ( 30) SS BOND : angle 0.79849 ( 60) hydrogen bonds : bond 0.03013 ( 714) hydrogen bonds : angle 4.34319 ( 1944) link_ALPHA1-2 : bond 0.00785 ( 6) link_ALPHA1-2 : angle 2.42101 ( 18) link_ALPHA1-3 : bond 0.01390 ( 11) link_ALPHA1-3 : angle 3.09231 ( 33) link_ALPHA1-6 : bond 0.01133 ( 9) link_ALPHA1-6 : angle 1.87262 ( 27) link_BETA1-4 : bond 0.00507 ( 56) link_BETA1-4 : angle 1.75357 ( 168) link_BETA1-6 : bond 0.00576 ( 12) link_BETA1-6 : angle 1.53823 ( 36) link_NAG-ASN : bond 0.00760 ( 33) link_NAG-ASN : angle 3.44433 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8250 (pp) REVERT: H 72 ASP cc_start: 0.7094 (t0) cc_final: 0.6759 (t0) REVERT: L 13 LEU cc_start: 0.8555 (tp) cc_final: 0.8210 (tt) REVERT: L 36 TYR cc_start: 0.7545 (m-80) cc_final: 0.7297 (m-80) REVERT: L 79 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6439 (mp0) REVERT: L 100 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8185 (mp10) REVERT: T 4 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8050 (pp) REVERT: T 42 GLN cc_start: 0.6646 (mp10) cc_final: 0.5977 (mp10) REVERT: S 73 ASP cc_start: 0.7640 (t0) cc_final: 0.7158 (t0) REVERT: S 82 GLU cc_start: 0.7693 (tm-30) cc_final: 0.6698 (tm-30) REVERT: D 38 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7628 (ptm160) REVERT: D 72 ASP cc_start: 0.7908 (t0) cc_final: 0.7540 (t0) REVERT: D 75 LYS cc_start: 0.9111 (pttt) cc_final: 0.8834 (pmmt) REVERT: E 17 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7924 (mp0) REVERT: E 27 GLN cc_start: 0.8747 (pm20) cc_final: 0.8138 (pm20) REVERT: B 130 ASP cc_start: 0.8665 (t0) cc_final: 0.8353 (t0) REVERT: b 286 ILE cc_start: 0.8627 (pt) cc_final: 0.8293 (pp) REVERT: b 287 GLU cc_start: 0.8643 (mp0) cc_final: 0.8000 (mp0) REVERT: b 331 GLN cc_start: 0.7297 (pp30) cc_final: 0.6870 (pp30) REVERT: P 24 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7959 (ttm110) REVERT: P 78 MET cc_start: 0.8140 (ttt) cc_final: 0.7502 (tmm) REVERT: O 3 GLN cc_start: 0.8718 (pm20) cc_final: 0.8415 (pm20) REVERT: O 46 GLU cc_start: 0.8305 (tt0) cc_final: 0.7851 (pt0) REVERT: O 73 ASP cc_start: 0.6686 (t0) cc_final: 0.6400 (t70) REVERT: F 45 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7217 (pp) REVERT: F 46 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7729 (tp30) REVERT: F 72 ASP cc_start: 0.8297 (t0) cc_final: 0.8006 (t0) REVERT: G 17 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8473 (tm-30) REVERT: C 100 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8030 (pm20) REVERT: C 125 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7924 (ttpp) REVERT: c 335 GLN cc_start: 0.8413 (mt0) cc_final: 0.7765 (pm20) REVERT: c 396 GLU cc_start: 0.8920 (mp0) cc_final: 0.8652 (mp0) REVERT: R 24 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7731 (ttm110) REVERT: R 100 GLN cc_start: 0.8622 (mm110) cc_final: 0.8284 (mp10) REVERT: R 103 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7847 (ttm-80) REVERT: Q 62 GLN cc_start: 0.8794 (tp40) cc_final: 0.8560 (tp40) REVERT: Q 65 GLN cc_start: 0.8461 (mt0) cc_final: 0.8120 (mt0) outliers start: 41 outliers final: 28 residues processed: 391 average time/residue: 0.7486 time to fit residues: 322.1304 Evaluate side-chains 384 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 352 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 83 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 135 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 ASN a 409 ASN T 31 ASN b 295 ASN O 120 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071228 restraints weight = 41544.588| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.55 r_work: 0.2929 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20352 Z= 0.139 Angle : 0.766 13.251 27863 Z= 0.352 Chirality : 0.044 0.495 3404 Planarity : 0.004 0.082 3260 Dihedral : 9.468 115.694 5024 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.31 % Allowed : 22.47 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2250 helix: 1.10 (0.28), residues: 384 sheet: 0.81 (0.20), residues: 684 loop : -0.59 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 24 TYR 0.030 0.001 TYR R 49 PHE 0.013 0.001 PHE D 78 TRP 0.012 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00321 (20195) covalent geometry : angle 0.71450 (27422) SS BOND : bond 0.00308 ( 30) SS BOND : angle 0.88280 ( 60) hydrogen bonds : bond 0.03108 ( 714) hydrogen bonds : angle 4.32126 ( 1944) link_ALPHA1-2 : bond 0.00785 ( 6) link_ALPHA1-2 : angle 2.46774 ( 18) link_ALPHA1-3 : bond 0.01355 ( 11) link_ALPHA1-3 : angle 3.08019 ( 33) link_ALPHA1-6 : bond 0.01115 ( 9) link_ALPHA1-6 : angle 1.90483 ( 27) link_BETA1-4 : bond 0.00484 ( 56) link_BETA1-4 : angle 1.75461 ( 168) link_BETA1-6 : bond 0.00532 ( 12) link_BETA1-6 : angle 1.55266 ( 36) link_NAG-ASN : bond 0.00743 ( 33) link_NAG-ASN : angle 3.42049 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7575.55 seconds wall clock time: 129 minutes 38.32 seconds (7778.32 seconds total)