Starting phenix.real_space_refine on Sat Sep 12 08:55:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrw_21372/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_2026/6vrw_21372.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vrw_21372/09_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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.92, per 1000 atoms: 0.20 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: 0.97 Conformation dependent library (CDL) restraints added in 482.9 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: 0.42 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: 2.35 Time building geometry restraints manager: 1.27 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 - 14.14: 6841 14.14 - 28.29: 963 28.29 - 42.43: 293 42.43 - 56.58: 42 56.58 - 70.72: 18 Dihedral angle restraints: 8157 sinusoidal: 3336 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 8154 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: 0.05 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 13.936 70.719 4932 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/Z covalent geometry : bond 0.00722 / 0.34 (14838) covalent geometry : angle 0.93078 / 0.45 (20136) SS BOND : bond 0.01287 / 0.83 ( 33) SS BOND : angle 2.39679 / 1.71 ( 66) hydrogen bonds : bond 0.18902 / 12.79 ( 381) hydrogen bonds : angle 8.00800 / 5.45 ( 1044) link_ALPHA1-3 : bond 0.00898 / 0.45 ( 3) link_ALPHA1-3 : angle 2.80889 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00093 / 0.05 ( 3) link_ALPHA1-6 : angle 1.59009 / 0.75 ( 9) link_BETA1-4 : bond 0.00550 / 0.34 ( 27) link_BETA1-4 : angle 3.07961 / 1.84 ( 81) link_NAG-ASN : bond 0.00819 / 0.50 ( 63) link_NAG-ASN : angle 4.49722 / 3.26 ( 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 : 0.436 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: 0.1265 time to fit residues: 21.6235 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 : 0.528 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052214 restraints weight = 53581.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054241 restraints weight = 27591.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055648 restraints weight = 18207.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056600 restraints weight = 13782.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057233 restraints weight = 11327.671| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14967 Z= 0.131 Angle : 0.730 11.102 20490 Z= 0.329 Chirality : 0.051 0.438 2553 Planarity : 0.003 0.030 2433 Dihedral : 5.218 21.309 1770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.94 % Allowed : 11.02 % Favored : 88.04 % 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: -4.01 (0.17), residues: 1623 helix: -2.10 (0.22), residues: 351 sheet: -2.67 (0.20), residues: 444 loop : -2.90 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 273 TYR 0.007 0.001 TYR D 223 PHE 0.012 0.001 PHE E 651 TRP 0.008 0.001 TRP G 427 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14838) covalent geometry : angle 0.64480 / 0.31 (20136) SS BOND : bond 0.00391 / 0.27 ( 33) SS BOND : angle 1.42808 / 1.00 ( 66) hydrogen bonds : bond 0.03962 / 2.60 ( 381) hydrogen bonds : angle 5.74504 / 3.87 ( 1044) link_ALPHA1-3 : bond 0.00945 / 0.47 ( 3) link_ALPHA1-3 : angle 1.82047 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00467 / 0.24 ( 3) link_ALPHA1-6 : angle 1.48247 / 0.73 ( 9) link_BETA1-4 : bond 0.00281 / 0.17 ( 27) link_BETA1-4 : angle 1.74575 / 1.07 ( 81) link_NAG-ASN : bond 0.00574 / 0.35 ( 63) link_NAG-ASN : angle 3.34825 / 2.47 ( 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 96 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: B 575 GLN cc_start: 0.8917 (tt0) cc_final: 0.8361 (tm-30) REVERT: B 626 MET cc_start: 0.8495 (tpp) cc_final: 0.8129 (tpp) REVERT: B 634 GLU cc_start: 0.8951 (mp0) cc_final: 0.8594 (mp0) REVERT: A 104 MET cc_start: 0.8807 (ttt) cc_final: 0.8552 (ttt) REVERT: C 575 GLN cc_start: 0.8669 (tt0) cc_final: 0.8311 (tm-30) REVERT: C 634 GLU cc_start: 0.8727 (mp0) cc_final: 0.8437 (mp0) REVERT: D 195 ASN cc_start: 0.8524 (p0) cc_final: 0.8207 (p0) REVERT: E 575 GLN cc_start: 0.8778 (tt0) cc_final: 0.8300 (tm-30) REVERT: E 626 MET cc_start: 0.8483 (tpp) cc_final: 0.7978 (tpp) REVERT: E 634 GLU cc_start: 0.8997 (mp0) cc_final: 0.8521 (mp0) outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 0.1083 time to fit residues: 15.6365 Evaluate side-chains 76 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 434 MET 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: 6.9990 chunk 4 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 55 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052217 restraints weight = 54014.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.054269 restraints weight = 27506.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.055664 restraints weight = 18089.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056611 restraints weight = 13683.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057282 restraints weight = 11255.803| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14967 Z= 0.128 Angle : 0.698 10.746 20490 Z= 0.316 Chirality : 0.051 0.408 2553 Planarity : 0.003 0.029 2433 Dihedral : 5.229 34.720 1770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.34 % Allowed : 13.51 % Favored : 85.15 % 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: -3.33 (0.18), residues: 1623 helix: -1.05 (0.26), residues: 351 sheet: -2.41 (0.20), 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 0.006 0.001 TYR D 223 PHE 0.012 0.001 PHE A 382 TRP 0.009 0.001 TRP E 631 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14838) covalent geometry : angle 0.62078 / 0.30 (20136) SS BOND : bond 0.00297 / 0.20 ( 33) SS BOND : angle 1.70746 / 1.17 ( 66) hydrogen bonds : bond 0.03426 / 2.24 ( 381) hydrogen bonds : angle 5.11440 / 3.45 ( 1044) link_ALPHA1-3 : bond 0.01025 / 0.52 ( 3) link_ALPHA1-3 : angle 1.98137 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00373 / 0.19 ( 3) link_ALPHA1-6 : angle 1.39373 / 0.66 ( 9) link_BETA1-4 : bond 0.00286 / 0.18 ( 27) link_BETA1-4 : angle 1.69990 / 1.05 ( 81) link_NAG-ASN : bond 0.00526 / 0.32 ( 63) link_NAG-ASN : angle 3.04609 / 2.27 ( 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: 20 poor density : 86 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: G 423 ILE cc_start: 0.9155 (mt) cc_final: 0.8927 (mt) REVERT: B 575 GLN cc_start: 0.8909 (tt0) cc_final: 0.8309 (tm-30) REVERT: B 626 MET cc_start: 0.8418 (tpp) cc_final: 0.8044 (tpp) REVERT: B 634 GLU cc_start: 0.8913 (mp0) cc_final: 0.8521 (mp0) REVERT: C 575 GLN cc_start: 0.8683 (tt0) cc_final: 0.8352 (tm-30) REVERT: C 634 GLU cc_start: 0.8642 (mp0) cc_final: 0.8418 (mp0) REVERT: D 195 ASN cc_start: 0.8550 (p0) cc_final: 0.8259 (p0) REVERT: E 575 GLN cc_start: 0.8775 (tt0) cc_final: 0.8306 (tm-30) REVERT: E 626 MET cc_start: 0.8446 (tpp) cc_final: 0.7968 (tpp) REVERT: E 634 GLU cc_start: 0.8937 (mp0) cc_final: 0.8484 (mp0) outliers start: 20 outliers final: 9 residues processed: 103 average time/residue: 0.1092 time to fit residues: 17.5856 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 : 0.542 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052486 restraints weight = 53716.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054454 restraints weight = 28584.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055793 restraints weight = 19272.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056716 restraints weight = 14817.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057341 restraints weight = 12299.808| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1765 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= 0.173 Angle : 0.716 10.634 20490 Z= 0.324 Chirality : 0.051 0.407 2553 Planarity : 0.003 0.034 2433 Dihedral : 5.085 30.508 1770 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.95 % Allowed : 14.78 % Favored : 83.27 % 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: -2.94 (0.19), residues: 1623 helix: -0.39 (0.27), residues: 351 sheet: -2.34 (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 A 298 TYR 0.007 0.001 TYR G 223 PHE 0.014 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/Z covalent geometry : bond 0.00402 / 0.17 (14838) covalent geometry : angle 0.64748 / 0.31 (20136) SS BOND : bond 0.00394 / 0.25 ( 33) SS BOND : angle 1.45218 / 1.02 ( 66) hydrogen bonds : bond 0.03403 / 2.24 ( 381) hydrogen bonds : angle 5.01673 / 3.40 ( 1044) link_ALPHA1-3 : bond 0.01018 / 0.51 ( 3) link_ALPHA1-3 : angle 2.06884 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00323 / 0.16 ( 3) link_ALPHA1-6 : angle 1.44234 / 0.69 ( 9) link_BETA1-4 : bond 0.00217 / 0.14 ( 27) link_BETA1-4 : angle 1.69091 / 1.04 ( 81) link_NAG-ASN : bond 0.00481 / 0.30 ( 63) link_NAG-ASN : angle 2.93269 / 2.20 ( 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 98 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 423 ILE cc_start: 0.9222 (mt) cc_final: 0.9007 (mt) REVERT: B 575 GLN cc_start: 0.8911 (tt0) cc_final: 0.8395 (tm-30) REVERT: B 626 MET cc_start: 0.8358 (tpp) cc_final: 0.8065 (tpp) REVERT: B 634 GLU cc_start: 0.8854 (mp0) cc_final: 0.8440 (mp0) REVERT: B 647 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 575 GLN cc_start: 0.8707 (tt0) cc_final: 0.8459 (tm-30) REVERT: E 575 GLN cc_start: 0.8773 (tt0) cc_final: 0.8354 (tm-30) REVERT: E 626 MET cc_start: 0.8512 (tpp) cc_final: 0.8227 (tpp) REVERT: E 634 GLU cc_start: 0.8867 (mp0) cc_final: 0.8460 (mp0) outliers start: 29 outliers final: 21 residues processed: 96 average time/residue: 0.1082 time to fit residues: 16.1905 Evaluate side-chains 82 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU 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 G residue 488 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 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 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 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: 0.0070 chunk 62 optimal weight: 0.0980 chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054375 restraints weight = 52880.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056429 restraints weight = 27835.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057821 restraints weight = 18576.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058735 restraints weight = 14153.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059417 restraints weight = 11722.877| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14967 Z= 0.100 Angle : 0.658 10.259 20490 Z= 0.293 Chirality : 0.050 0.392 2553 Planarity : 0.003 0.030 2433 Dihedral : 4.765 25.794 1770 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.75 % Allowed : 16.40 % Favored : 81.85 % 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: -2.59 (0.19), residues: 1623 helix: 0.03 (0.28), residues: 351 sheet: -2.18 (0.22), residues: 399 loop : -2.26 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 476 TYR 0.003 0.000 TYR A 223 PHE 0.010 0.001 PHE D 382 TRP 0.009 0.001 TRP E 631 HIS 0.004 0.000 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14838) covalent geometry : angle 0.59150 / 0.28 (20136) SS BOND : bond 0.00429 / 0.29 ( 33) SS BOND : angle 1.32528 / 0.96 ( 66) hydrogen bonds : bond 0.02781 / 1.83 ( 381) hydrogen bonds : angle 4.72548 / 3.21 ( 1044) link_ALPHA1-3 : bond 0.01051 / 0.53 ( 3) link_ALPHA1-3 : angle 1.86515 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00350 / 0.18 ( 3) link_ALPHA1-6 : angle 1.41307 / 0.68 ( 9) link_BETA1-4 : bond 0.00380 / 0.23 ( 27) link_BETA1-4 : angle 1.62945 / 1.00 ( 81) link_NAG-ASN : bond 0.00519 / 0.32 ( 63) link_NAG-ASN : angle 2.75438 / 2.07 ( 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: 26 poor density : 77 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8373 (mmp) cc_final: 0.8150 (mmp) REVERT: G 426 MET cc_start: 0.8014 (ttp) cc_final: 0.7756 (ttp) REVERT: B 575 GLN cc_start: 0.8829 (tt0) cc_final: 0.8272 (tm-30) REVERT: B 626 MET cc_start: 0.8403 (tpp) cc_final: 0.8103 (tpp) REVERT: B 634 GLU cc_start: 0.8762 (mp0) cc_final: 0.8370 (mp0) REVERT: C 575 GLN cc_start: 0.8663 (tt0) cc_final: 0.8389 (tm-30) REVERT: E 575 GLN cc_start: 0.8720 (tt0) cc_final: 0.8268 (tm-30) REVERT: E 626 MET cc_start: 0.8409 (tpp) cc_final: 0.8043 (tpp) REVERT: E 634 GLU cc_start: 0.8798 (mp0) cc_final: 0.8436 (mp0) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.1056 time to fit residues: 16.8845 Evaluate side-chains 80 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL 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 38 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 142 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.065658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053867 restraints weight = 52994.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055877 restraints weight = 28138.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057251 restraints weight = 18873.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058185 restraints weight = 14435.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058814 restraints weight = 11922.303| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14967 Z= 0.121 Angle : 0.666 10.110 20490 Z= 0.298 Chirality : 0.050 0.384 2553 Planarity : 0.003 0.032 2433 Dihedral : 4.732 29.093 1770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.55 % Allowed : 15.93 % Favored : 81.52 % 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: -2.41 (0.20), residues: 1623 helix: 0.39 (0.29), residues: 351 sheet: -2.10 (0.22), residues: 399 loop : -2.24 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 633 TYR 0.018 0.001 TYR D 486 PHE 0.011 0.001 PHE D 382 TRP 0.007 0.001 TRP B 631 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14838) covalent geometry : angle 0.60172 / 0.28 (20136) SS BOND : bond 0.00367 / 0.25 ( 33) SS BOND : angle 1.34447 / 0.97 ( 66) hydrogen bonds : bond 0.02858 / 1.87 ( 381) hydrogen bonds : angle 4.58933 / 3.12 ( 1044) link_ALPHA1-3 : bond 0.00988 / 0.50 ( 3) link_ALPHA1-3 : angle 1.91179 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00324 / 0.16 ( 3) link_ALPHA1-6 : angle 1.44212 / 0.69 ( 9) link_BETA1-4 : bond 0.00266 / 0.16 ( 27) link_BETA1-4 : angle 1.63126 / 1.01 ( 81) link_NAG-ASN : bond 0.00467 / 0.29 ( 63) link_NAG-ASN : angle 2.72031 / 2.05 ( 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 105 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8125 (mmp) cc_final: 0.7903 (mmp) REVERT: G 426 MET cc_start: 0.8106 (ttp) cc_final: 0.7860 (ttp) REVERT: B 575 GLN cc_start: 0.8857 (tt0) cc_final: 0.8315 (tm-30) REVERT: B 626 MET cc_start: 0.8408 (tpp) cc_final: 0.8107 (tpp) REVERT: B 634 GLU cc_start: 0.8772 (mp0) cc_final: 0.8392 (mp0) REVERT: C 575 GLN cc_start: 0.8693 (tt0) cc_final: 0.8428 (tm-30) REVERT: D 486 TYR cc_start: 0.8508 (m-80) cc_final: 0.8260 (m-80) REVERT: E 575 GLN cc_start: 0.8748 (tt0) cc_final: 0.8286 (tm-30) REVERT: E 626 MET cc_start: 0.8450 (tpp) cc_final: 0.8142 (tpp) REVERT: E 634 GLU cc_start: 0.8804 (mp0) cc_final: 0.8444 (mp0) outliers start: 38 outliers final: 29 residues processed: 102 average time/residue: 0.1113 time to fit residues: 17.7132 Evaluate side-chains 94 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 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 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 38 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 205 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053258 restraints weight = 52618.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055240 restraints weight = 27995.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056579 restraints weight = 18843.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057513 restraints weight = 14444.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058161 restraints weight = 11949.446| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14967 Z= 0.143 Angle : 0.675 10.223 20490 Z= 0.303 Chirality : 0.050 0.385 2553 Planarity : 0.003 0.035 2433 Dihedral : 4.767 28.115 1770 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % Favored : 81.18 % 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: 0.65 (0.30), residues: 351 sheet: -2.11 (0.21), residues: 420 loop : -2.15 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 298 TYR 0.010 0.001 TYR D 486 PHE 0.011 0.001 PHE D 382 TRP 0.006 0.001 TRP E 631 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (14838) covalent geometry : angle 0.61213 / 0.29 (20136) SS BOND : bond 0.00385 / 0.26 ( 33) SS BOND : angle 1.42735 / 1.00 ( 66) hydrogen bonds : bond 0.02944 / 1.94 ( 381) hydrogen bonds : angle 4.59547 / 3.13 ( 1044) link_ALPHA1-3 : bond 0.01000 / 0.50 ( 3) link_ALPHA1-3 : angle 1.95042 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00309 / 0.16 ( 3) link_ALPHA1-6 : angle 1.44817 / 0.69 ( 9) link_BETA1-4 : bond 0.00233 / 0.14 ( 27) link_BETA1-4 : angle 1.64827 / 1.01 ( 81) link_NAG-ASN : bond 0.00447 / 0.28 ( 63) link_NAG-ASN : angle 2.69815 / 2.04 ( 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 102 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 GLN cc_start: 0.8873 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 634 GLU cc_start: 0.8799 (mp0) cc_final: 0.8455 (mp0) REVERT: C 575 GLN cc_start: 0.8747 (tt0) cc_final: 0.8480 (tm-30) REVERT: D 475 MET cc_start: 0.7304 (ptt) cc_final: 0.6983 (ptt) REVERT: E 575 GLN cc_start: 0.8768 (tt0) cc_final: 0.8302 (tm-30) REVERT: E 626 MET cc_start: 0.8500 (tpp) cc_final: 0.8225 (tpp) REVERT: E 634 GLU cc_start: 0.8792 (mp0) cc_final: 0.8281 (mp0) REVERT: E 654 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8279 (mm-30) outliers start: 37 outliers final: 32 residues processed: 98 average time/residue: 0.1120 time to fit residues: 17.1770 Evaluate side-chains 95 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 38 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 205 CYS 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: 0.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.053978 restraints weight = 52579.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056004 restraints weight = 27729.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057372 restraints weight = 18597.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058261 restraints weight = 14197.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058942 restraints weight = 11773.622| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2280 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= 0.112 Angle : 0.653 10.082 20490 Z= 0.292 Chirality : 0.050 0.380 2553 Planarity : 0.003 0.083 2433 Dihedral : 4.661 26.977 1770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.08 % Allowed : 16.87 % Favored : 81.05 % 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: 0.76 (0.30), residues: 351 sheet: -1.94 (0.22), residues: 399 loop : -2.16 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 633 TYR 0.011 0.001 TYR D 486 PHE 0.010 0.001 PHE D 382 TRP 0.006 0.001 TRP B 631 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (14838) covalent geometry : angle 0.59186 / 0.28 (20136) SS BOND : bond 0.00393 / 0.26 ( 33) SS BOND : angle 1.26152 / 0.89 ( 66) hydrogen bonds : bond 0.02733 / 1.80 ( 381) hydrogen bonds : angle 4.50630 / 3.07 ( 1044) link_ALPHA1-3 : bond 0.00986 / 0.49 ( 3) link_ALPHA1-3 : angle 1.85722 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00327 / 0.16 ( 3) link_ALPHA1-6 : angle 1.43444 / 0.69 ( 9) link_BETA1-4 : bond 0.00300 / 0.19 ( 27) link_BETA1-4 : angle 1.62113 / 0.99 ( 81) link_NAG-ASN : bond 0.00470 / 0.29 ( 63) link_NAG-ASN : angle 2.64942 / 2.00 ( 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 101 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 302 MET cc_start: 0.8098 (mmp) cc_final: 0.7825 (mmp) REVERT: G 426 MET cc_start: 0.8136 (ttp) cc_final: 0.7851 (ttp) REVERT: B 575 GLN cc_start: 0.8856 (tt0) cc_final: 0.8267 (tm-30) REVERT: B 634 GLU cc_start: 0.8707 (mp0) cc_final: 0.8064 (mp0) REVERT: B 647 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 575 GLN cc_start: 0.8738 (tt0) cc_final: 0.8475 (tm-30) REVERT: E 575 GLN cc_start: 0.8758 (tt0) cc_final: 0.8288 (tm-30) REVERT: E 634 GLU cc_start: 0.8675 (mp0) cc_final: 0.8205 (mp0) REVERT: E 654 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8293 (mm-30) outliers start: 31 outliers final: 28 residues processed: 98 average time/residue: 0.1105 time to fit residues: 16.7488 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL 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 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 C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 38 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 205 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052826 restraints weight = 53247.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054804 restraints weight = 28298.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056128 restraints weight = 19078.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057054 restraints weight = 14653.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057666 restraints weight = 12145.950| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14967 Z= 0.173 Angle : 0.700 10.329 20490 Z= 0.319 Chirality : 0.051 0.383 2553 Planarity : 0.003 0.052 2433 Dihedral : 4.790 28.391 1770 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.15 % Allowed : 17.07 % Favored : 80.78 % 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: -2.21 (0.20), residues: 1623 helix: 0.81 (0.30), residues: 351 sheet: -2.05 (0.22), residues: 399 loop : -2.19 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 633 TYR 0.011 0.001 TYR D 486 PHE 0.012 0.002 PHE D 382 TRP 0.008 0.001 TRP A 427 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (14838) covalent geometry : angle 0.64001 / 0.30 (20136) SS BOND : bond 0.00385 / 0.25 ( 33) SS BOND : angle 1.43170 / 1.01 ( 66) hydrogen bonds : bond 0.03083 / 2.04 ( 381) hydrogen bonds : angle 4.62619 / 3.16 ( 1044) link_ALPHA1-3 : bond 0.00962 / 0.48 ( 3) link_ALPHA1-3 : angle 2.00134 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00299 / 0.15 ( 3) link_ALPHA1-6 : angle 1.45573 / 0.70 ( 9) link_BETA1-4 : bond 0.00206 / 0.13 ( 27) link_BETA1-4 : angle 1.67515 / 1.03 ( 81) link_NAG-ASN : bond 0.00447 / 0.28 ( 63) link_NAG-ASN : angle 2.70657 / 2.05 ( 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 98 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 426 MET cc_start: 0.8256 (ttp) cc_final: 0.8028 (ttp) REVERT: B 575 GLN cc_start: 0.8890 (tt0) cc_final: 0.8328 (tm-30) REVERT: C 575 GLN cc_start: 0.8768 (tt0) cc_final: 0.8469 (tm-30) REVERT: D 475 MET cc_start: 0.7370 (ptt) cc_final: 0.7072 (ptt) REVERT: D 486 TYR cc_start: 0.8595 (m-80) cc_final: 0.8358 (m-80) REVERT: E 575 GLN cc_start: 0.8786 (tt0) cc_final: 0.8309 (tm-30) outliers start: 32 outliers final: 31 residues processed: 95 average time/residue: 0.1120 time to fit residues: 16.8749 Evaluate side-chains 91 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL 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 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 38 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 205 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051318 restraints weight = 53715.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053221 restraints weight = 29005.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054517 restraints weight = 19768.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055401 restraints weight = 15309.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056020 restraints weight = 12802.129| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.006 0.048 14967 Z= 0.269 Angle : 0.794 10.746 20490 Z= 0.367 Chirality : 0.053 0.400 2553 Planarity : 0.003 0.039 2433 Dihedral : 5.233 31.152 1770 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.49 % Allowed : 16.67 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.35 (0.20), residues: 1623 helix: 0.86 (0.30), residues: 351 sheet: -2.14 (0.21), residues: 429 loop : -2.34 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 633 TYR 0.009 0.001 TYR D 223 PHE 0.015 0.002 PHE D 93 TRP 0.013 0.001 TRP A 427 HIS 0.009 0.002 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (14838) covalent geometry : angle 0.73419 / 0.35 (20136) SS BOND : bond 0.00408 / 0.26 ( 33) SS BOND : angle 1.75260 / 1.24 ( 66) hydrogen bonds : bond 0.03705 / 2.48 ( 381) hydrogen bonds : angle 4.92592 / 3.36 ( 1044) link_ALPHA1-3 : bond 0.01004 / 0.50 ( 3) link_ALPHA1-3 : angle 2.15975 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00264 / 0.13 ( 3) link_ALPHA1-6 : angle 1.47711 / 0.70 ( 9) link_BETA1-4 : bond 0.00210 / 0.14 ( 27) link_BETA1-4 : angle 1.78902 / 1.09 ( 81) link_NAG-ASN : bond 0.00521 / 0.33 ( 63) link_NAG-ASN : angle 2.85068 / 2.15 ( 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 96 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 217 TYR cc_start: 0.8303 (m-10) cc_final: 0.8073 (m-10) REVERT: B 575 GLN cc_start: 0.8909 (tt0) cc_final: 0.8377 (tm-30) REVERT: A 434 MET cc_start: 0.8743 (ptp) cc_final: 0.8501 (ptp) REVERT: C 575 GLN cc_start: 0.8819 (tt0) cc_final: 0.8502 (tm-30) REVERT: D 475 MET cc_start: 0.7472 (ptt) cc_final: 0.7206 (ptt) REVERT: E 575 GLN cc_start: 0.8829 (tt0) cc_final: 0.8358 (tm-30) outliers start: 37 outliers final: 30 residues processed: 93 average time/residue: 0.1049 time to fit residues: 16.0537 Evaluate side-chains 87 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 488 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 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 205 CYS 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 640 ASP 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: 3.9990 chunk 155 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053291 restraints weight = 52771.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055284 restraints weight = 28363.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056635 restraints weight = 19176.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057559 restraints weight = 14735.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058176 restraints weight = 12238.220| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14967 Z= 0.120 Angle : 0.682 10.325 20490 Z= 0.308 Chirality : 0.051 0.400 2553 Planarity : 0.003 0.033 2433 Dihedral : 4.885 27.276 1770 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.75 % Allowed : 17.34 % Favored : 80.91 % 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: -2.14 (0.20), residues: 1623 helix: 1.00 (0.30), residues: 351 sheet: -2.03 (0.22), residues: 399 loop : -2.20 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 298 TYR 0.011 0.001 TYR D 486 PHE 0.010 0.001 PHE A 317 TRP 0.017 0.001 TRP G 427 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14838) covalent geometry : angle 0.62116 / 0.29 (20136) SS BOND : bond 0.00381 / 0.25 ( 33) SS BOND : angle 1.27767 / 0.92 ( 66) hydrogen bonds : bond 0.03015 / 2.03 ( 381) hydrogen bonds : angle 4.68503 / 3.20 ( 1044) link_ALPHA1-3 : bond 0.00921 / 0.46 ( 3) link_ALPHA1-3 : angle 1.84789 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00317 / 0.16 ( 3) link_ALPHA1-6 : angle 1.42772 / 0.68 ( 9) link_BETA1-4 : bond 0.00332 / 0.20 ( 27) link_BETA1-4 : angle 1.67767 / 1.01 ( 81) link_NAG-ASN : bond 0.00484 / 0.30 ( 63) link_NAG-ASN : angle 2.70636 / 2.04 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.10 seconds wall clock time: 33 minutes 25.32 seconds (2005.32 seconds total)