Starting phenix.real_space_refine on Wed Mar 4 16:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrw_21372/03_2026/6vrw_21372.cif" } resolution = 3.71 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= 0.011 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9117 2.51 5 N 2370 2.21 5 O 2982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s 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: 14568 Number of models: 1 Model: "" Number of chains: 36 Chain: "G" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3430 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 5 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3430 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 5 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3430 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 5 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14568 At special positions: 0 Unit cell: (119.893, 130.503, 124.137, 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 99 16.00 O 2982 8.00 N 2370 7.00 C 9117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=1.98 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.05 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.07 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA U 3 " - " MAN U 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA U 3 " - " MAN U 5 " " BMA c 3 " - " MAN c 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1088 " - " ASN A 88 " " NAG A1156 " - " ASN A 156 " " NAG A1234 " - " ASN A 234 " " NAG A1276 " - " ASN A 276 " " NAG A1301 " - " ASN A 301 " " NAG A1356 " - " ASN A 356 " " NAG A1362 " - " ASN A 362 " " NAG A1386 " - " ASN A 386 " " NAG A1442 " - " ASN A 442 " " NAG A1448 " - " ASN A 448 " " NAG A1502 " - " ASN A 502 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1611 " - " ASN C 611 " " NAG C1637 " - " ASN C 637 " " NAG D1088 " - " ASN D 88 " " NAG D1156 " - " ASN D 156 " " NAG D1234 " - " ASN D 234 " " NAG D1276 " - " ASN D 276 " " NAG D1301 " - " ASN D 301 " " NAG D1356 " - " ASN D 356 " " NAG D1362 " - " ASN D 362 " " NAG D1386 " - " ASN D 386 " " NAG D1442 " - " ASN D 442 " " NAG D1448 " - " ASN D 448 " " NAG D1502 " - " ASN D 502 " " NAG E1611 " - " ASN E 611 " " NAG E1637 " - " ASN E 637 " " NAG F 1 " - " ASN G 160 " " NAG G1088 " - " ASN G 88 " " NAG G1156 " - " ASN G 156 " " NAG G1234 " - " ASN G 234 " " NAG G1276 " - " ASN G 276 " " NAG G1301 " - " ASN G 301 " " NAG G1356 " - " ASN G 356 " " NAG G1362 " - " ASN G 362 " " NAG G1386 " - " ASN G 386 " " NAG G1442 " - " ASN G 442 " " NAG G1448 " - " ASN G 448 " " NAG G1502 " - " ASN G 502 " " NAG H 1 " - " ASN G 130 " " NAG I 1 " - " ASN G 197 " " NAG J 1 " - " ASN G 230 " " NAG K 1 " - " ASN G 241 " " NAG L 1 " - " ASN G 332 " " NAG M 1 " - " ASN G 262 " " NAG N 1 " - " ASN G 289 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 130 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 230 " " NAG S 1 " - " ASN A 241 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 289 " " NAG W 1 " - " ASN D 160 " " NAG X 1 " - " ASN D 130 " " NAG Y 1 " - " ASN D 197 " " NAG Z 1 " - " ASN D 230 " " NAG a 1 " - " ASN D 241 " " NAG b 1 " - " ASN D 332 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 289 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 418.3 milliseconds 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 21.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.661A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 removed outlier: 3.904A pdb=" N LYS G 340 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR G 341 " --> pdb=" O LYS G 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.690A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.698A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 529 through 534 removed outlier: 4.338A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.821A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.799A pdb=" N ASP B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.967A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 657 removed outlier: 3.605A pdb=" N LEU B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.662A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.903A pdb=" N LYS A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.690A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.699A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 522 Processing helix chain 'C' and resid 529 through 534 removed outlier: 4.338A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 595 removed outlier: 3.821A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 removed outlier: 3.799A pdb=" N ASP C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.966A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 657 removed outlier: 3.606A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 116 removed outlier: 3.662A pdb=" N HIS D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP D 107 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.902A pdb=" N LYS D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.690A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.699A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 522 Processing helix chain 'E' and resid 529 through 534 removed outlier: 4.339A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.822A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 3.799A pdb=" N ASP E 624 " --> pdb=" O ASN E 620 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN E 625 " --> pdb=" O GLU E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.968A pdb=" N ASP E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG E 633 " --> pdb=" O MET E 629 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 657 removed outlier: 3.605A pdb=" N LEU E 645 " --> pdb=" O THR E 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 4.910A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.554A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.934A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.722A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.225A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 272 through 273 removed outlier: 3.558A pdb=" N VAL G 286 " --> pdb=" O LEU G 452 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.518A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 301 through 312 removed outlier: 6.986A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.805A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.554A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.934A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.722A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.225A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.558A pdb=" N VAL A 286 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.517A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.987A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.924A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.553A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.934A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.723A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 239 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AC8, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC9, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.224A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 272 through 273 removed outlier: 3.558A pdb=" N VAL D 286 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.518A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 421 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 292 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 301 through 312 removed outlier: 6.986A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1044 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: 2.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4532 1.36 - 1.49: 4010 1.49 - 1.62: 6164 1.62 - 1.75: 0 1.75 - 1.88: 132 Bond restraints: 14838 Sorted by residual: bond pdb=" C5 MAN U 4 " pdb=" O5 MAN U 4 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" C5 MAN M 4 " pdb=" O5 MAN M 4 " ideal model delta sigma weight residual 1.418 1.480 -0.062 2.00e-02 2.50e+03 9.71e+00 bond pdb=" C5 MAN c 4 " pdb=" O5 MAN c 4 " ideal model delta sigma weight residual 1.418 1.480 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C1 NAG G1442 " pdb=" O5 NAG G1442 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C1 NAG D1442 " pdb=" O5 NAG D1442 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 14833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19104 1.95 - 3.90: 878 3.90 - 5.85: 102 5.85 - 7.80: 34 7.80 - 9.76: 18 Bond angle restraints: 20136 Sorted by residual: angle pdb=" C TRP G 427 " pdb=" N GLN G 428 " pdb=" CA GLN G 428 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C TRP D 427 " pdb=" N GLN D 428 " pdb=" CA GLN D 428 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TRP A 427 " pdb=" N GLN A 428 " pdb=" CA GLN A 428 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C ASN D 386 " pdb=" N THR D 387 " pdb=" CA THR D 387 " ideal model delta sigma weight residual 122.61 128.52 -5.91 1.56e+00 4.11e-01 1.44e+01 angle pdb=" C ASN A 386 " pdb=" N THR A 387 " pdb=" CA THR A 387 " ideal model delta sigma weight residual 122.61 128.50 -5.89 1.56e+00 4.11e-01 1.43e+01 ... (remaining 20131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 9377 23.71 - 47.43: 619 47.43 - 71.14: 129 71.14 - 94.85: 18 94.85 - 118.56: 12 Dihedral angle restraints: 10155 sinusoidal: 5334 harmonic: 4821 Sorted by residual: dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual 93.00 152.78 -59.78 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " pdb=" SG CYS D 239 " pdb=" CB CYS D 239 " ideal model delta sinusoidal sigma weight residual 93.00 152.76 -59.76 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 152.75 -59.75 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 10152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2195 0.090 - 0.180: 304 0.180 - 0.270: 33 0.270 - 0.360: 6 0.360 - 0.450: 15 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG A1088 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A1088 " pdb=" O5 NAG A1088 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C1 NAG D1088 " pdb=" ND2 ASN D 88 " pdb=" C2 NAG D1088 " pdb=" O5 NAG D1088 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C1 NAG G1088 " pdb=" ND2 ASN G 88 " pdb=" C2 NAG G1088 " pdb=" O5 NAG G1088 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 2550 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 245 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL A 245 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 245 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 246 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 171 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ARG D 171 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG D 171 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU D 172 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 171 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C ARG G 171 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG G 171 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU G 172 " -0.009 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4364 2.82 - 3.34: 12263 3.34 - 3.86: 22752 3.86 - 4.38: 24118 4.38 - 4.90: 42790 Nonbonded interactions: 106287 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" O CYS C 604 " model vdw 2.301 3.040 nonbonded pdb=" O THR G 450 " pdb=" OG1 THR G 450 " model vdw 2.304 3.040 nonbonded pdb=" O THR A 450 " pdb=" OG1 THR A 450 " model vdw 2.306 3.040 nonbonded pdb=" O THR D 450 " pdb=" OG1 THR D 450 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR G 37 " pdb=" O CYS B 604 " model vdw 2.309 3.040 ... (remaining 106282 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' } ncs_group { reference = chain 'M' selection = chain 'U' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.007 0.076 14967 Z= 0.341 Angle : 1.048 14.838 20490 Z= 0.483 Chirality : 0.068 0.450 2553 Planarity : 0.005 0.039 2433 Dihedral : 15.783 118.563 6930 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.40 % Allowed : 8.20 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.95 (0.15), residues: 1623 helix: -3.68 (0.15), residues: 330 sheet: -2.87 (0.20), residues: 453 loop : -3.37 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.009 0.001 TYR A 191 PHE 0.016 0.002 PHE D 317 TRP 0.010 0.002 TRP A 45 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00722 (14838) covalent geometry : angle 0.93078 (20136) SS BOND : bond 0.01287 ( 33) SS BOND : angle 2.39679 ( 66) hydrogen bonds : bond 0.18902 ( 381) hydrogen bonds : angle 8.00800 ( 1044) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 2.80889 ( 9) link_ALPHA1-6 : bond 0.00093 ( 3) link_ALPHA1-6 : angle 1.59009 ( 9) link_BETA1-4 : bond 0.00550 ( 27) link_BETA1-4 : angle 3.07961 ( 81) link_NAG-ASN : bond 0.00819 ( 63) link_NAG-ASN : angle 4.49722 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 575 GLN cc_start: 0.8867 (tt0) cc_final: 0.8496 (tm-30) REVERT: B 626 MET cc_start: 0.8388 (tpp) cc_final: 0.8132 (tpp) REVERT: A 104 MET cc_start: 0.8825 (ttt) cc_final: 0.8605 (ttt) REVERT: C 575 GLN cc_start: 0.8662 (tt0) cc_final: 0.8429 (tm-30) REVERT: C 603 ILE cc_start: 0.9252 (mt) cc_final: 0.8943 (mp) REVERT: C 634 GLU cc_start: 0.8834 (mp0) cc_final: 0.8502 (mp0) REVERT: C 635 ILE cc_start: 0.9143 (tp) cc_final: 0.8822 (tp) REVERT: D 104 MET cc_start: 0.9008 (ttt) cc_final: 0.8785 (ttt) REVERT: D 195 ASN cc_start: 0.8541 (p0) cc_final: 0.8148 (p0) REVERT: D 449 ILE cc_start: 0.8211 (mt) cc_final: 0.7958 (pt) REVERT: E 575 GLN cc_start: 0.8765 (tt0) cc_final: 0.8384 (tm-30) REVERT: E 603 ILE cc_start: 0.9057 (mt) cc_final: 0.8716 (mp) REVERT: E 626 MET cc_start: 0.8504 (tpp) cc_final: 0.8191 (tpp) REVERT: E 654 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8498 (mm-30) outliers start: 6 outliers final: 3 residues processed: 117 average time/residue: 0.1428 time to fit residues: 23.8344 Evaluate side-chains 73 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain E residue 513 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052197 restraints weight = 53468.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054242 restraints weight = 27317.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055618 restraints weight = 17994.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056571 restraints weight = 13622.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057264 restraints weight = 11178.420| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14967 Z= 0.133 Angle : 0.744 11.156 20490 Z= 0.333 Chirality : 0.052 0.454 2553 Planarity : 0.003 0.030 2433 Dihedral : 12.810 102.152 3768 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.87 % Allowed : 10.89 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.02 (0.17), residues: 1623 helix: -2.12 (0.22), residues: 351 sheet: -2.68 (0.20), residues: 444 loop : -2.91 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 432 TYR 0.007 0.001 TYR D 223 PHE 0.013 0.001 PHE E 651 TRP 0.008 0.001 TRP E 631 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00296 (14838) covalent geometry : angle 0.65589 (20136) SS BOND : bond 0.00325 ( 33) SS BOND : angle 1.41740 ( 66) hydrogen bonds : bond 0.03984 ( 381) hydrogen bonds : angle 5.76695 ( 1044) link_ALPHA1-3 : bond 0.02277 ( 3) link_ALPHA1-3 : angle 2.81797 ( 9) link_ALPHA1-6 : bond 0.00473 ( 3) link_ALPHA1-6 : angle 1.69601 ( 9) link_BETA1-4 : bond 0.00299 ( 27) link_BETA1-4 : angle 1.90407 ( 81) link_NAG-ASN : bond 0.00567 ( 63) link_NAG-ASN : angle 3.38590 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: B 575 GLN cc_start: 0.8912 (tt0) cc_final: 0.8360 (tm-30) REVERT: B 626 MET cc_start: 0.8497 (tpp) cc_final: 0.8134 (tpp) REVERT: B 634 GLU cc_start: 0.8951 (mp0) cc_final: 0.8598 (mp0) REVERT: A 104 MET cc_start: 0.8806 (ttt) cc_final: 0.8534 (ttt) REVERT: C 575 GLN cc_start: 0.8667 (tt0) cc_final: 0.8313 (tm-30) REVERT: C 634 GLU cc_start: 0.8727 (mp0) cc_final: 0.8440 (mp0) REVERT: D 195 ASN cc_start: 0.8522 (p0) cc_final: 0.8203 (p0) REVERT: E 575 GLN cc_start: 0.8777 (tt0) cc_final: 0.8302 (tm-30) REVERT: E 626 MET cc_start: 0.8484 (tpp) cc_final: 0.7982 (tpp) REVERT: E 634 GLU cc_start: 0.8994 (mp0) cc_final: 0.8521 (mp0) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 0.1232 time to fit residues: 17.4048 Evaluate side-chains 75 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052606 restraints weight = 53901.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054680 restraints weight = 27473.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056086 restraints weight = 18019.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057046 restraints weight = 13587.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057733 restraints weight = 11144.031| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14967 Z= 0.121 Angle : 0.710 10.669 20490 Z= 0.317 Chirality : 0.052 0.409 2553 Planarity : 0.003 0.028 2433 Dihedral : 11.581 91.507 3768 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.21 % Allowed : 12.97 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.34 (0.18), residues: 1623 helix: -1.14 (0.25), residues: 351 sheet: -2.36 (0.21), residues: 423 loop : -2.62 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 432 TYR 0.005 0.001 TYR D 223 PHE 0.011 0.001 PHE A 382 TRP 0.008 0.001 TRP E 631 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00268 (14838) covalent geometry : angle 0.62976 (20136) SS BOND : bond 0.00389 ( 33) SS BOND : angle 1.64210 ( 66) hydrogen bonds : bond 0.03351 ( 381) hydrogen bonds : angle 5.11341 ( 1044) link_ALPHA1-3 : bond 0.02315 ( 3) link_ALPHA1-3 : angle 2.94647 ( 9) link_ALPHA1-6 : bond 0.00742 ( 3) link_ALPHA1-6 : angle 1.51925 ( 9) link_BETA1-4 : bond 0.00339 ( 27) link_BETA1-4 : angle 1.80093 ( 81) link_NAG-ASN : bond 0.00542 ( 63) link_NAG-ASN : angle 3.08496 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: G 423 ILE cc_start: 0.9174 (mt) cc_final: 0.8963 (mt) REVERT: B 575 GLN cc_start: 0.8901 (tt0) cc_final: 0.8327 (tm-30) REVERT: B 626 MET cc_start: 0.8451 (tpp) cc_final: 0.8076 (tpp) REVERT: B 634 GLU cc_start: 0.8910 (mp0) cc_final: 0.8517 (mp0) REVERT: C 575 GLN cc_start: 0.8671 (tt0) cc_final: 0.8330 (tm-30) REVERT: C 634 GLU cc_start: 0.8629 (mp0) cc_final: 0.8418 (mp0) REVERT: D 195 ASN cc_start: 0.8538 (p0) cc_final: 0.8258 (p0) REVERT: E 575 GLN cc_start: 0.8748 (tt0) cc_final: 0.8290 (tm-30) REVERT: E 626 MET cc_start: 0.8430 (tpp) cc_final: 0.7951 (tpp) REVERT: E 634 GLU cc_start: 0.8936 (mp0) cc_final: 0.8499 (mp0) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 0.1107 time to fit residues: 17.8448 Evaluate side-chains 78 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052903 restraints weight = 53686.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054883 restraints weight = 28389.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056241 restraints weight = 19115.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057130 restraints weight = 14628.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057793 restraints weight = 12183.103| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14967 Z= 0.159 Angle : 0.719 10.516 20490 Z= 0.321 Chirality : 0.052 0.404 2553 Planarity : 0.003 0.033 2433 Dihedral : 10.862 84.215 3768 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.68 % Allowed : 14.58 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.95 (0.19), residues: 1623 helix: -0.45 (0.27), residues: 351 sheet: -2.31 (0.20), residues: 429 loop : -2.44 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 633 TYR 0.006 0.001 TYR D 223 PHE 0.014 0.001 PHE D 382 TRP 0.008 0.001 TRP B 631 HIS 0.007 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00363 (14838) covalent geometry : angle 0.64778 (20136) SS BOND : bond 0.00495 ( 33) SS BOND : angle 1.52005 ( 66) hydrogen bonds : bond 0.03330 ( 381) hydrogen bonds : angle 4.93917 ( 1044) link_ALPHA1-3 : bond 0.02290 ( 3) link_ALPHA1-3 : angle 3.01578 ( 9) link_ALPHA1-6 : bond 0.00884 ( 3) link_ALPHA1-6 : angle 1.55692 ( 9) link_BETA1-4 : bond 0.00225 ( 27) link_BETA1-4 : angle 1.75218 ( 81) link_NAG-ASN : bond 0.00485 ( 63) link_NAG-ASN : angle 2.95575 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 423 ILE cc_start: 0.9206 (mt) cc_final: 0.8991 (mt) REVERT: B 575 GLN cc_start: 0.8907 (tt0) cc_final: 0.8401 (tm-30) REVERT: B 626 MET cc_start: 0.8475 (tpp) cc_final: 0.8147 (tpp) REVERT: B 634 GLU cc_start: 0.8853 (mp0) cc_final: 0.8442 (mp0) REVERT: B 647 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8542 (tm-30) REVERT: C 575 GLN cc_start: 0.8684 (tt0) cc_final: 0.8426 (tm-30) REVERT: D 195 ASN cc_start: 0.8482 (p0) cc_final: 0.8230 (p0) REVERT: E 575 GLN cc_start: 0.8766 (tt0) cc_final: 0.8343 (tm-30) REVERT: E 626 MET cc_start: 0.8472 (tpp) cc_final: 0.8065 (tpp) REVERT: E 634 GLU cc_start: 0.8852 (mp0) cc_final: 0.8462 (mp0) outliers start: 25 outliers final: 16 residues processed: 95 average time/residue: 0.1238 time to fit residues: 17.9667 Evaluate side-chains 80 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052421 restraints weight = 53475.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054392 restraints weight = 28478.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055718 restraints weight = 19221.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056601 restraints weight = 14770.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057284 restraints weight = 12303.968| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14967 Z= 0.178 Angle : 0.728 10.633 20490 Z= 0.325 Chirality : 0.052 0.411 2553 Planarity : 0.003 0.034 2433 Dihedral : 10.397 76.560 3768 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.35 % Allowed : 15.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.19), residues: 1623 helix: 0.03 (0.28), residues: 351 sheet: -2.23 (0.21), residues: 429 loop : -2.40 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 298 TYR 0.007 0.001 TYR D 223 PHE 0.013 0.002 PHE D 382 TRP 0.008 0.001 TRP B 631 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00409 (14838) covalent geometry : angle 0.65908 (20136) SS BOND : bond 0.00334 ( 33) SS BOND : angle 1.52619 ( 66) hydrogen bonds : bond 0.03323 ( 381) hydrogen bonds : angle 4.90597 ( 1044) link_ALPHA1-3 : bond 0.02590 ( 3) link_ALPHA1-3 : angle 3.33491 ( 9) link_ALPHA1-6 : bond 0.01065 ( 3) link_ALPHA1-6 : angle 1.70834 ( 9) link_BETA1-4 : bond 0.00232 ( 27) link_BETA1-4 : angle 1.75318 ( 81) link_NAG-ASN : bond 0.00471 ( 63) link_NAG-ASN : angle 2.88580 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 426 MET cc_start: 0.7932 (ttp) cc_final: 0.7632 (ttp) REVERT: B 575 GLN cc_start: 0.8863 (tt0) cc_final: 0.8361 (tm-30) REVERT: B 626 MET cc_start: 0.8402 (tpp) cc_final: 0.8096 (tpp) REVERT: B 634 GLU cc_start: 0.8822 (mp0) cc_final: 0.8428 (mp0) REVERT: B 647 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 575 GLN cc_start: 0.8736 (tt0) cc_final: 0.8479 (tm-30) REVERT: E 575 GLN cc_start: 0.8785 (tt0) cc_final: 0.8325 (tm-30) REVERT: E 626 MET cc_start: 0.8529 (tpp) cc_final: 0.8121 (tpp) REVERT: E 634 GLU cc_start: 0.8854 (mp0) cc_final: 0.8488 (mp0) outliers start: 35 outliers final: 21 residues processed: 102 average time/residue: 0.1117 time to fit residues: 17.8235 Evaluate side-chains 83 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 142 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052320 restraints weight = 53363.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054281 restraints weight = 28637.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055621 restraints weight = 19348.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056502 restraints weight = 14857.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057159 restraints weight = 12401.452| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14967 Z= 0.179 Angle : 0.729 10.600 20490 Z= 0.326 Chirality : 0.052 0.410 2553 Planarity : 0.003 0.036 2433 Dihedral : 10.171 72.836 3768 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.69 % Allowed : 16.53 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.20), residues: 1623 helix: 0.29 (0.29), residues: 351 sheet: -2.18 (0.21), residues: 429 loop : -2.38 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 633 TYR 0.017 0.001 TYR D 486 PHE 0.013 0.001 PHE D 382 TRP 0.009 0.001 TRP B 631 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00413 (14838) covalent geometry : angle 0.66157 (20136) SS BOND : bond 0.00360 ( 33) SS BOND : angle 1.50052 ( 66) hydrogen bonds : bond 0.03253 ( 381) hydrogen bonds : angle 4.86357 ( 1044) link_ALPHA1-3 : bond 0.02682 ( 3) link_ALPHA1-3 : angle 3.39526 ( 9) link_ALPHA1-6 : bond 0.01080 ( 3) link_ALPHA1-6 : angle 1.76131 ( 9) link_BETA1-4 : bond 0.00240 ( 27) link_BETA1-4 : angle 1.75097 ( 81) link_NAG-ASN : bond 0.00457 ( 63) link_NAG-ASN : angle 2.87020 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 GLN cc_start: 0.8878 (tt0) cc_final: 0.8373 (tm-30) REVERT: B 626 MET cc_start: 0.8443 (tpp) cc_final: 0.8185 (tpp) REVERT: B 634 GLU cc_start: 0.8791 (mp0) cc_final: 0.8397 (mp0) REVERT: B 647 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8529 (tm-30) REVERT: C 575 GLN cc_start: 0.8740 (tt0) cc_final: 0.8504 (tm-30) REVERT: E 575 GLN cc_start: 0.8794 (tt0) cc_final: 0.8330 (tm-30) REVERT: E 626 MET cc_start: 0.8495 (tpp) cc_final: 0.8128 (tpp) REVERT: E 634 GLU cc_start: 0.8827 (mp0) cc_final: 0.8481 (mp0) outliers start: 40 outliers final: 29 residues processed: 104 average time/residue: 0.1101 time to fit residues: 17.9422 Evaluate side-chains 89 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053637 restraints weight = 52338.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055651 restraints weight = 27667.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057025 restraints weight = 18491.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057961 restraints weight = 14108.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058619 restraints weight = 11623.674| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14967 Z= 0.119 Angle : 0.688 10.404 20490 Z= 0.304 Chirality : 0.051 0.401 2553 Planarity : 0.003 0.033 2433 Dihedral : 9.626 64.259 3768 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.75 % Allowed : 17.61 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.20), residues: 1623 helix: 0.56 (0.29), residues: 351 sheet: -1.95 (0.21), residues: 429 loop : -2.29 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 633 TYR 0.014 0.001 TYR D 486 PHE 0.010 0.001 PHE D 382 TRP 0.009 0.001 TRP E 631 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (14838) covalent geometry : angle 0.62009 (20136) SS BOND : bond 0.00472 ( 33) SS BOND : angle 1.37502 ( 66) hydrogen bonds : bond 0.02806 ( 381) hydrogen bonds : angle 4.62864 ( 1044) link_ALPHA1-3 : bond 0.03037 ( 3) link_ALPHA1-3 : angle 3.68370 ( 9) link_ALPHA1-6 : bond 0.01146 ( 3) link_ALPHA1-6 : angle 1.69502 ( 9) link_BETA1-4 : bond 0.00315 ( 27) link_BETA1-4 : angle 1.68978 ( 81) link_NAG-ASN : bond 0.00496 ( 63) link_NAG-ASN : angle 2.77988 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 426 MET cc_start: 0.8122 (ttp) cc_final: 0.7828 (ttp) REVERT: B 575 GLN cc_start: 0.8859 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 626 MET cc_start: 0.8427 (tpp) cc_final: 0.8176 (tpp) REVERT: B 634 GLU cc_start: 0.8743 (mp0) cc_final: 0.8424 (mp0) REVERT: B 647 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8527 (tm-30) REVERT: C 575 GLN cc_start: 0.8720 (tt0) cc_final: 0.8471 (tm-30) REVERT: E 575 GLN cc_start: 0.8754 (tt0) cc_final: 0.8284 (tm-30) REVERT: E 626 MET cc_start: 0.8458 (tpp) cc_final: 0.8108 (tpp) REVERT: E 634 GLU cc_start: 0.8757 (mp0) cc_final: 0.8256 (mp0) outliers start: 26 outliers final: 22 residues processed: 89 average time/residue: 0.1130 time to fit residues: 15.6577 Evaluate side-chains 82 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053371 restraints weight = 52877.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055373 restraints weight = 28241.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056741 restraints weight = 18968.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057657 restraints weight = 14495.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058274 restraints weight = 12016.630| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14967 Z= 0.136 Angle : 0.696 10.254 20490 Z= 0.309 Chirality : 0.051 0.394 2553 Planarity : 0.003 0.049 2433 Dihedral : 9.526 60.907 3768 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.02 % Allowed : 17.67 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.27 (0.20), residues: 1623 helix: 0.69 (0.29), residues: 351 sheet: -1.91 (0.21), residues: 429 loop : -2.28 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 633 TYR 0.012 0.001 TYR D 486 PHE 0.011 0.001 PHE A 317 TRP 0.009 0.001 TRP A 427 HIS 0.010 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00311 (14838) covalent geometry : angle 0.62840 (20136) SS BOND : bond 0.00380 ( 33) SS BOND : angle 1.48717 ( 66) hydrogen bonds : bond 0.02914 ( 381) hydrogen bonds : angle 4.55903 ( 1044) link_ALPHA1-3 : bond 0.03039 ( 3) link_ALPHA1-3 : angle 3.74512 ( 9) link_ALPHA1-6 : bond 0.01126 ( 3) link_ALPHA1-6 : angle 1.69901 ( 9) link_BETA1-4 : bond 0.00295 ( 27) link_BETA1-4 : angle 1.69273 ( 81) link_NAG-ASN : bond 0.00465 ( 63) link_NAG-ASN : angle 2.76684 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8146 (mmp) cc_final: 0.7820 (mmp) REVERT: G 426 MET cc_start: 0.8216 (ttp) cc_final: 0.7965 (ttp) REVERT: B 575 GLN cc_start: 0.8869 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 626 MET cc_start: 0.8449 (tpp) cc_final: 0.8190 (tpp) REVERT: B 634 GLU cc_start: 0.8738 (mp0) cc_final: 0.8430 (mp0) REVERT: B 647 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 575 GLN cc_start: 0.8735 (tt0) cc_final: 0.8500 (tm-30) REVERT: E 575 GLN cc_start: 0.8762 (tt0) cc_final: 0.8289 (tm-30) REVERT: E 634 GLU cc_start: 0.8710 (mp0) cc_final: 0.8202 (mp0) outliers start: 30 outliers final: 28 residues processed: 92 average time/residue: 0.1065 time to fit residues: 15.5482 Evaluate side-chains 91 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052519 restraints weight = 53355.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054497 restraints weight = 28428.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055831 restraints weight = 19160.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056746 restraints weight = 14722.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057372 restraints weight = 12225.024| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14967 Z= 0.191 Angle : 0.726 10.453 20490 Z= 0.326 Chirality : 0.052 0.397 2553 Planarity : 0.003 0.037 2433 Dihedral : 9.597 59.717 3768 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.28 % Allowed : 17.54 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.27 (0.20), residues: 1623 helix: 0.77 (0.30), residues: 351 sheet: -2.03 (0.21), residues: 450 loop : -2.24 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 633 TYR 0.011 0.001 TYR D 486 PHE 0.012 0.002 PHE A 317 TRP 0.012 0.001 TRP A 427 HIS 0.019 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00439 (14838) covalent geometry : angle 0.65942 (20136) SS BOND : bond 0.00394 ( 33) SS BOND : angle 1.56753 ( 66) hydrogen bonds : bond 0.03182 ( 381) hydrogen bonds : angle 4.65441 ( 1044) link_ALPHA1-3 : bond 0.03079 ( 3) link_ALPHA1-3 : angle 3.81126 ( 9) link_ALPHA1-6 : bond 0.01123 ( 3) link_ALPHA1-6 : angle 1.77995 ( 9) link_BETA1-4 : bond 0.00260 ( 27) link_BETA1-4 : angle 1.73153 ( 81) link_NAG-ASN : bond 0.00447 ( 63) link_NAG-ASN : angle 2.79239 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8231 (mmp) cc_final: 0.7905 (mmp) REVERT: G 426 MET cc_start: 0.8193 (ttp) cc_final: 0.7984 (ttp) REVERT: B 575 GLN cc_start: 0.8892 (tt0) cc_final: 0.8326 (tm-30) REVERT: B 626 MET cc_start: 0.8503 (tpp) cc_final: 0.8034 (tpp) REVERT: B 634 GLU cc_start: 0.8861 (mp0) cc_final: 0.8066 (mp0) REVERT: B 647 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 575 GLN cc_start: 0.8769 (tt0) cc_final: 0.8477 (tm-30) REVERT: E 575 GLN cc_start: 0.8795 (tt0) cc_final: 0.8322 (tm-30) outliers start: 34 outliers final: 31 residues processed: 95 average time/residue: 0.1106 time to fit residues: 16.5216 Evaluate side-chains 90 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053797 restraints weight = 52903.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055817 restraints weight = 28166.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057191 restraints weight = 18949.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058078 restraints weight = 14521.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058744 restraints weight = 12085.469| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14967 Z= 0.122 Angle : 0.694 10.190 20490 Z= 0.310 Chirality : 0.051 0.394 2553 Planarity : 0.003 0.067 2433 Dihedral : 9.323 58.535 3768 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.02 % Allowed : 17.74 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.20), residues: 1623 helix: 0.85 (0.30), residues: 351 sheet: -1.95 (0.22), residues: 399 loop : -2.19 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG B 633 TYR 0.006 0.001 TYR D 486 PHE 0.010 0.001 PHE A 317 TRP 0.019 0.001 TRP A 427 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00273 (14838) covalent geometry : angle 0.62898 (20136) SS BOND : bond 0.00393 ( 33) SS BOND : angle 1.31884 ( 66) hydrogen bonds : bond 0.02898 ( 381) hydrogen bonds : angle 4.55760 ( 1044) link_ALPHA1-3 : bond 0.03243 ( 3) link_ALPHA1-3 : angle 3.95149 ( 9) link_ALPHA1-6 : bond 0.01146 ( 3) link_ALPHA1-6 : angle 1.66189 ( 9) link_BETA1-4 : bond 0.00354 ( 27) link_BETA1-4 : angle 1.68977 ( 81) link_NAG-ASN : bond 0.00490 ( 63) link_NAG-ASN : angle 2.72515 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8104 (mmp) cc_final: 0.7863 (mmp) REVERT: G 426 MET cc_start: 0.8191 (ttp) cc_final: 0.7980 (ttp) REVERT: B 575 GLN cc_start: 0.8867 (tt0) cc_final: 0.8262 (tm-30) REVERT: B 626 MET cc_start: 0.8454 (tpp) cc_final: 0.8123 (tpp) REVERT: B 647 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8503 (tm-30) REVERT: C 575 GLN cc_start: 0.8752 (tt0) cc_final: 0.8439 (tm-30) REVERT: E 575 GLN cc_start: 0.8749 (tt0) cc_final: 0.8285 (tm-30) REVERT: E 626 MET cc_start: 0.8764 (tpp) cc_final: 0.8327 (tpp) outliers start: 30 outliers final: 28 residues processed: 96 average time/residue: 0.1017 time to fit residues: 15.8672 Evaluate side-chains 90 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053494 restraints weight = 52513.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055494 restraints weight = 28054.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056844 restraints weight = 18940.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057748 restraints weight = 14531.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058359 restraints weight = 12083.341| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14967 Z= 0.138 Angle : 0.693 10.245 20490 Z= 0.310 Chirality : 0.051 0.388 2553 Planarity : 0.003 0.043 2433 Dihedral : 9.278 57.762 3768 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.08 % Allowed : 17.81 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.11 (0.20), residues: 1623 helix: 0.92 (0.30), residues: 351 sheet: -1.83 (0.22), residues: 429 loop : -2.23 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 633 TYR 0.016 0.001 TYR D 486 PHE 0.011 0.001 PHE D 382 TRP 0.018 0.001 TRP A 427 HIS 0.020 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (14838) covalent geometry : angle 0.62704 (20136) SS BOND : bond 0.00386 ( 33) SS BOND : angle 1.37875 ( 66) hydrogen bonds : bond 0.02967 ( 381) hydrogen bonds : angle 4.52748 ( 1044) link_ALPHA1-3 : bond 0.03320 ( 3) link_ALPHA1-3 : angle 4.05038 ( 9) link_ALPHA1-6 : bond 0.01116 ( 3) link_ALPHA1-6 : angle 1.63917 ( 9) link_BETA1-4 : bond 0.00302 ( 27) link_BETA1-4 : angle 1.69089 ( 81) link_NAG-ASN : bond 0.00459 ( 63) link_NAG-ASN : angle 2.72421 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.31 seconds wall clock time: 32 minutes 58.73 seconds (1978.73 seconds total)