Starting phenix.real_space_refine on Fri Mar 6 22:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sju_54954/03_2026/9sju_54954.map" } resolution = 2.08 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= 0.007 sd= 0.314 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: 6 Type Number sf(0) Gaussians Fe 24 7.16 5 Mg 24 5.21 5 S 168 5.16 5 C 21312 2.51 5 N 5952 2.21 5 O 7872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35352 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' FE': 4, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "K" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "N" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "O" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "P" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "Q" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "S" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "T" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "V" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "W" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "X" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "Y" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Restraints were copied for chains: D, F, I, J, R, C, E, G, H, K, L, M, N, O, P, Q, S, T, V, W, X, Y Residues with excluded nonbonded symmetry interactions: 24 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb="FE FE A 203 " occ=0.25 residue: pdb="FE FE A 204 " occ=0.25 residue: pdb="FE FE A 205 " occ=0.25 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb="FE FE D 203 " occ=0.25 residue: pdb="FE FE D 204 " occ=0.25 residue: pdb="FE FE D 205 " occ=0.25 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb="FE FE F 203 " occ=0.25 residue: pdb="FE FE F 204 " occ=0.25 residue: pdb="FE FE F 205 " occ=0.25 ... (remaining 12 not shown) Time building chain proxies: 3.56, per 1000 atoms: 0.10 Number of scatterers: 35352 At special positions: 0 Unit cell: (136.752, 136.752, 136.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 24 26.01 S 168 16.00 Mg 24 11.99 O 7872 8.00 N 5952 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 39 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 39 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU C 137 " --> pdb=" O HIS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 39 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 39 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 39 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU F 137 " --> pdb=" O HIS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 39 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 121 Processing helix chain 'G' and resid 123 through 156 removed outlier: 5.744A pdb=" N SER G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU G 137 " --> pdb=" O HIS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 39 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 121 Processing helix chain 'H' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU H 137 " --> pdb=" O HIS H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 39 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU I 137 " --> pdb=" O HIS I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 39 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU J 137 " --> pdb=" O HIS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 39 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU K 137 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.565A pdb=" N GLU K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 39 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU L 137 " --> pdb=" O HIS L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 39 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU M 137 " --> pdb=" O HIS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU M 164 " --> pdb=" O SER M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 39 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU N 137 " --> pdb=" O HIS N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 39 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU O 137 " --> pdb=" O HIS O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU O 164 " --> pdb=" O SER O 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 39 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU P 137 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU P 164 " --> pdb=" O SER P 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 39 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU Q 137 " --> pdb=" O HIS Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU Q 164 " --> pdb=" O SER Q 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 39 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER R 136 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU R 137 " --> pdb=" O HIS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 39 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER S 136 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU S 137 " --> pdb=" O HIS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU S 164 " --> pdb=" O SER S 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 39 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU T 137 " --> pdb=" O HIS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU T 164 " --> pdb=" O SER T 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 39 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER V 136 " --> pdb=" O THR V 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU V 137 " --> pdb=" O HIS V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU V 164 " --> pdb=" O SER V 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 39 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER W 136 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU W 137 " --> pdb=" O HIS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU W 164 " --> pdb=" O SER W 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 39 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU X 137 " --> pdb=" O HIS X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 171 removed outlier: 3.566A pdb=" N GLU X 164 " --> pdb=" O SER X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 39 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 156 removed outlier: 5.743A pdb=" N SER Y 136 " --> pdb=" O THR Y 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU Y 137 " --> pdb=" O HIS Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 171 removed outlier: 3.565A pdb=" N GLU Y 164 " --> pdb=" O SER Y 160 " (cutoff:3.500A) 2688 hydrogen bonds defined for protein. 8064 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: 7.16 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11568 1.34 - 1.46: 6118 1.46 - 1.58: 16754 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" CB PHE M 38 " pdb=" CG PHE M 38 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.28e-01 bond pdb=" CB PHE X 38 " pdb=" CG PHE X 38 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 5.82e-01 bond pdb=" CB PHE D 38 " pdb=" CG PHE D 38 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 5.82e-01 bond pdb=" CB PHE O 38 " pdb=" CG PHE O 38 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 5.80e-01 bond pdb=" CB PHE E 38 " pdb=" CG PHE E 38 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 5.80e-01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 44674 1.25 - 2.49: 1648 2.49 - 3.74: 214 3.74 - 4.98: 120 4.98 - 6.23: 72 Bond angle restraints: 46728 Sorted by residual: angle pdb=" N GLU S 91 " pdb=" CA GLU S 91 " pdb=" C GLU S 91 " ideal model delta sigma weight residual 110.80 117.03 -6.23 2.13e+00 2.20e-01 8.55e+00 angle pdb=" N GLU K 91 " pdb=" CA GLU K 91 " pdb=" C GLU K 91 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU O 91 " pdb=" CA GLU O 91 " pdb=" C GLU O 91 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU E 91 " pdb=" CA GLU E 91 " pdb=" C GLU E 91 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU P 91 " pdb=" CA GLU P 91 " pdb=" C GLU P 91 " ideal model delta sigma weight residual 110.80 116.97 -6.17 2.13e+00 2.20e-01 8.40e+00 ... (remaining 46723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 18288 17.90 - 35.80: 1968 35.80 - 53.70: 456 53.70 - 71.59: 216 71.59 - 89.49: 72 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA TRP N 90 " pdb=" C TRP N 90 " pdb=" N GLU N 91 " pdb=" CA GLU N 91 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TRP M 90 " pdb=" C TRP M 90 " pdb=" N GLU M 91 " pdb=" CA GLU M 91 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TRP X 90 " pdb=" C TRP X 90 " pdb=" N GLU X 91 " pdb=" CA GLU X 91 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2722 0.027 - 0.055: 1407 0.055 - 0.082: 431 0.082 - 0.110: 262 0.110 - 0.137: 98 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR X 36 " pdb=" N TYR X 36 " pdb=" C TYR X 36 " pdb=" CB TYR X 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA TYR P 36 " pdb=" N TYR P 36 " pdb=" C TYR P 36 " pdb=" CB TYR P 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA TYR L 36 " pdb=" N TYR L 36 " pdb=" C TYR L 36 " pdb=" CB TYR L 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 4917 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU V 131 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C GLU V 131 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU V 131 " -0.016 2.00e-02 2.50e+03 pdb=" N THR V 132 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 131 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C GLU Y 131 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU Y 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR Y 132 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 131 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C GLU I 131 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU I 131 " -0.015 2.00e-02 2.50e+03 pdb=" N THR I 132 " -0.014 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 108 0.98 - 1.96: 108 1.96 - 2.94: 16680 2.94 - 3.92: 117319 3.92 - 4.90: 202522 Warning: very small nonbonded interaction distances. Nonbonded interactions: 336737 Sorted by model distance: nonbonded pdb="FE FE F 204 " pdb="FE FE F 205 " model vdw 0.003 1.480 nonbonded pdb="FE FE R 201 " pdb="FE FE R 205 " model vdw 0.005 1.480 nonbonded pdb="FE FE R 204 " pdb="FE FE R 205 " model vdw 0.005 1.480 nonbonded pdb="FE FE F 203 " pdb="FE FE F 204 " model vdw 0.005 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE J 205 " model vdw 0.006 1.480 ... (remaining 336732 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 27.070 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.130 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:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.003 0.019 34704 Z= 0.173 Angle : 0.608 6.229 46728 Z= 0.334 Chirality : 0.042 0.137 4920 Planarity : 0.005 0.043 6144 Dihedral : 17.497 89.491 13032 Min Nonbonded Distance : 0.003 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 10.39 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.78 (0.13), residues: 4104 helix: 3.65 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.07 (0.27), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 153 TYR 0.023 0.003 TYR N 36 PHE 0.028 0.003 PHE E 38 TRP 0.009 0.003 TRP M 90 HIS 0.007 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00341 (34704) covalent geometry : angle 0.60818 (46728) hydrogen bonds : bond 0.07540 ( 2688) hydrogen bonds : angle 3.80432 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 683 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8394 (pptt) REVERT: C 50 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8393 (pptt) REVERT: D 50 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8395 (pptt) REVERT: F 50 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8395 (pptt) REVERT: G 50 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8396 (pptt) REVERT: I 50 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8392 (pptt) REVERT: J 50 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8394 (pptt) REVERT: N 50 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8402 (pptt) REVERT: O 50 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8394 (pptt) REVERT: Q 50 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8394 (pptt) REVERT: R 50 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (pptt) REVERT: S 50 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8402 (pptt) REVERT: T 50 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8392 (pptt) REVERT: V 50 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8388 (pptt) REVERT: W 50 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8391 (pptt) REVERT: X 50 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8395 (pptt) REVERT: Y 50 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8389 (pptt) outliers start: 48 outliers final: 24 residues processed: 707 average time/residue: 0.9546 time to fit residues: 767.9516 Evaluate side-chains 698 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 657 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 50 LYS Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 50 LYS Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 50 LYS Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 22 ASN A 57 HIS A 133 HIS B 10 HIS B 22 ASN B 57 HIS B 133 HIS C 10 HIS C 22 ASN C 57 HIS C 133 HIS D 10 HIS D 22 ASN D 57 HIS D 133 HIS E 10 HIS E 22 ASN E 57 HIS E 133 HIS F 10 HIS F 22 ASN F 57 HIS F 133 HIS G 10 HIS G 22 ASN G 57 HIS G 133 HIS H 10 HIS H 22 ASN H 57 HIS H 133 HIS I 10 HIS I 22 ASN I 57 HIS I 133 HIS J 10 HIS J 22 ASN J 57 HIS J 133 HIS K 10 HIS K 22 ASN K 57 HIS K 133 HIS L 10 HIS L 22 ASN L 57 HIS L 133 HIS M 10 HIS M 22 ASN M 57 HIS M 133 HIS N 10 HIS N 22 ASN N 57 HIS N 133 HIS O 10 HIS O 22 ASN O 57 HIS O 133 HIS P 10 HIS P 22 ASN P 57 HIS P 133 HIS Q 10 HIS Q 22 ASN Q 57 HIS Q 133 HIS R 10 HIS R 22 ASN R 57 HIS R 133 HIS S 10 HIS S 22 ASN S 57 HIS S 133 HIS T 10 HIS T 22 ASN T 57 HIS T 133 HIS V 10 HIS V 22 ASN V 57 HIS V 133 HIS W 10 HIS W 22 ASN W 57 HIS W 133 HIS X 10 HIS X 22 ASN X 57 HIS X 133 HIS Y 10 HIS Y 22 ASN Y 57 HIS Y 133 HIS Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121482 restraints weight = 24975.526| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.67 r_work: 0.3147 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2731 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.163 Angle : 0.607 6.006 46728 Z= 0.333 Chirality : 0.040 0.145 4920 Planarity : 0.005 0.042 6144 Dihedral : 7.635 56.970 4652 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.73 (0.13), residues: 4104 helix: 3.63 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 6 TYR 0.023 0.003 TYR K 36 PHE 0.025 0.003 PHE B 38 TRP 0.011 0.003 TRP H 90 HIS 0.009 0.002 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00323 (34704) covalent geometry : angle 0.60699 (46728) hydrogen bonds : bond 0.04839 ( 2688) hydrogen bonds : angle 3.60399 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 LYS cc_start: 0.8930 (tmmt) cc_final: 0.8725 (pptt) REVERT: V 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8882 (tmmt) REVERT: X 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8879 (tmmt) outliers start: 0 outliers final: 0 residues processed: 574 average time/residue: 0.9525 time to fit residues: 622.6786 Evaluate side-chains 580 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 288 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 364 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118287 restraints weight = 25005.035| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.63 r_work: 0.3109 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2688 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34704 Z= 0.193 Angle : 0.639 6.208 46728 Z= 0.351 Chirality : 0.042 0.153 4920 Planarity : 0.005 0.040 6144 Dihedral : 4.373 18.600 4512 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.46 % Allowed : 9.93 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.61 (0.13), residues: 4104 helix: 3.54 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.97 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 153 TYR 0.024 0.003 TYR O 36 PHE 0.027 0.003 PHE Q 38 TRP 0.013 0.004 TRP X 90 HIS 0.006 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00387 (34704) covalent geometry : angle 0.63892 (46728) hydrogen bonds : bond 0.05159 ( 2688) hydrogen bonds : angle 3.64835 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 624 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8937 (tmmt) REVERT: C 50 LYS cc_start: 0.9188 (ttpm) cc_final: 0.8937 (tmmt) REVERT: D 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8933 (tmmt) REVERT: F 50 LYS cc_start: 0.9175 (ttpm) cc_final: 0.8927 (tmmt) REVERT: G 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8923 (tmmt) REVERT: I 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8924 (tmmt) REVERT: J 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8936 (tmmt) REVERT: K 50 LYS cc_start: 0.9020 (tmmt) cc_final: 0.8785 (pptt) REVERT: N 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8936 (tmmt) REVERT: O 50 LYS cc_start: 0.9177 (ttpm) cc_final: 0.8932 (tmmt) REVERT: Q 50 LYS cc_start: 0.9193 (ttpm) cc_final: 0.8941 (tmmt) REVERT: R 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8923 (tmmt) REVERT: S 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8927 (tmmt) REVERT: T 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8929 (tmmt) REVERT: V 50 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8928 (tmmt) REVERT: W 50 LYS cc_start: 0.9178 (ttpm) cc_final: 0.8932 (tmmt) REVERT: X 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8926 (tmmt) REVERT: Y 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8924 (tmmt) outliers start: 17 outliers final: 17 residues processed: 641 average time/residue: 0.9480 time to fit residues: 692.0373 Evaluate side-chains 619 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 602 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 302 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS B 10 HIS B 133 HIS ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS G 10 HIS G 133 HIS H 10 HIS H 133 HIS ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 HIS ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 HIS ** K 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 HIS ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 HIS ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 HIS ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 HIS ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 HIS ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 HIS ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 GLN R 133 HIS ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 133 HIS ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 HIS ** X 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 HIS ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119661 restraints weight = 25001.837| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 0.61 r_work: 0.3116 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2693 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34704 Z= 0.169 Angle : 0.603 6.051 46728 Z= 0.331 Chirality : 0.041 0.149 4920 Planarity : 0.005 0.035 6144 Dihedral : 4.342 18.903 4512 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.19 % Allowed : 10.20 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.69 (0.13), residues: 4104 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.93 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 153 TYR 0.023 0.003 TYR N 36 PHE 0.025 0.003 PHE B 38 TRP 0.012 0.003 TRP K 90 HIS 0.005 0.001 HIS P 125 Details of bonding type rmsd covalent geometry : bond 0.00335 (34704) covalent geometry : angle 0.60303 (46728) hydrogen bonds : bond 0.04924 ( 2688) hydrogen bonds : angle 3.60276 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 596 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8935 (tmmt) REVERT: B 116 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8837 (tttm) REVERT: C 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8935 (tmmt) REVERT: D 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8929 (tmmt) REVERT: E 116 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8834 (tttm) REVERT: F 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8924 (tmmt) REVERT: G 50 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8919 (tmmt) REVERT: H 116 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8831 (tttm) REVERT: I 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8924 (tmmt) REVERT: J 50 LYS cc_start: 0.9177 (ttpm) cc_final: 0.8936 (tmmt) REVERT: K 50 LYS cc_start: 0.9038 (tmmt) cc_final: 0.8745 (pptt) REVERT: L 116 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8835 (tttm) REVERT: M 116 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8843 (tttm) REVERT: N 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8930 (tmmt) REVERT: O 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8929 (tmmt) REVERT: P 116 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8835 (tttm) REVERT: Q 50 LYS cc_start: 0.9184 (ttpm) cc_final: 0.8939 (tmmt) REVERT: R 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8919 (tmmt) REVERT: S 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8927 (tmmt) REVERT: T 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8927 (tmmt) REVERT: V 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8924 (tmmt) REVERT: W 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8926 (tmmt) REVERT: X 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8923 (tmmt) REVERT: Y 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8918 (tmmt) outliers start: 7 outliers final: 7 residues processed: 603 average time/residue: 0.9644 time to fit residues: 661.9061 Evaluate side-chains 603 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 596 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 176 optimal weight: 8.9990 chunk 260 optimal weight: 20.0000 chunk 266 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 367 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 382 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 GLN ** K 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.130386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.118169 restraints weight = 24984.708| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.63 r_work: 0.3102 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2679 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34704 Z= 0.192 Angle : 0.633 6.182 46728 Z= 0.348 Chirality : 0.042 0.152 4920 Planarity : 0.005 0.038 6144 Dihedral : 4.379 18.594 4512 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.52 % Allowed : 9.33 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.63 (0.13), residues: 4104 helix: 3.56 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.96 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 153 TYR 0.024 0.003 TYR E 36 PHE 0.027 0.003 PHE B 38 TRP 0.013 0.004 TRP L 90 HIS 0.006 0.001 HIS P 125 Details of bonding type rmsd covalent geometry : bond 0.00386 (34704) covalent geometry : angle 0.63270 (46728) hydrogen bonds : bond 0.05171 ( 2688) hydrogen bonds : angle 3.65102 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 583 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9171 (ttpm) cc_final: 0.8931 (tmmt) REVERT: C 50 LYS cc_start: 0.9178 (ttpm) cc_final: 0.8932 (tmmt) REVERT: D 50 LYS cc_start: 0.9171 (ttpm) cc_final: 0.8927 (tmmt) REVERT: F 50 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8922 (tmmt) REVERT: G 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8917 (tmmt) REVERT: I 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8918 (tmmt) REVERT: J 50 LYS cc_start: 0.9175 (ttpm) cc_final: 0.8932 (tmmt) REVERT: K 50 LYS cc_start: 0.9068 (tmmt) cc_final: 0.8743 (pptt) REVERT: N 50 LYS cc_start: 0.9172 (ttpm) cc_final: 0.8928 (tmmt) REVERT: O 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8926 (tmmt) REVERT: Q 50 LYS cc_start: 0.9184 (ttpm) cc_final: 0.8936 (tmmt) REVERT: R 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8919 (tmmt) REVERT: S 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8925 (tmmt) REVERT: T 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8925 (tmmt) REVERT: V 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8920 (tmmt) REVERT: W 50 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8922 (tmmt) REVERT: X 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8919 (tmmt) REVERT: Y 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8918 (tmmt) outliers start: 56 outliers final: 24 residues processed: 639 average time/residue: 0.9686 time to fit residues: 706.4773 Evaluate side-chains 615 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 591 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 99 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 HIS B 72 GLN ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 GLN ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 72 GLN ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN ** X 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117389 restraints weight = 24989.989| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.62 r_work: 0.3132 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work: 0.2725 rms_B_bonded: 4.20 restraints_weight: 0.1250 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 34704 Z= 0.227 Angle : 0.672 6.382 46728 Z= 0.369 Chirality : 0.044 0.156 4920 Planarity : 0.005 0.043 6144 Dihedral : 4.445 18.123 4512 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 8.85 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.55 (0.13), residues: 4104 helix: 3.49 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.01 (0.27), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG N 153 TYR 0.025 0.003 TYR V 36 PHE 0.030 0.004 PHE Q 38 TRP 0.014 0.004 TRP Y 90 HIS 0.006 0.002 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00461 (34704) covalent geometry : angle 0.67216 (46728) hydrogen bonds : bond 0.05463 ( 2688) hydrogen bonds : angle 3.71191 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 614 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9137 (ttpm) cc_final: 0.8873 (tmmt) REVERT: B 116 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8539 (tmmt) REVERT: C 50 LYS cc_start: 0.9140 (ttpm) cc_final: 0.8872 (tmmt) REVERT: D 50 LYS cc_start: 0.9141 (ttpm) cc_final: 0.8871 (tmmt) REVERT: E 116 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8541 (tmmt) REVERT: F 50 LYS cc_start: 0.9133 (ttpm) cc_final: 0.8866 (tmmt) REVERT: G 50 LYS cc_start: 0.9125 (ttpm) cc_final: 0.8865 (tmmt) REVERT: H 116 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8535 (tmmt) REVERT: I 50 LYS cc_start: 0.9123 (ttpm) cc_final: 0.8861 (tmmt) REVERT: J 50 LYS cc_start: 0.9140 (ttpm) cc_final: 0.8872 (tmmt) REVERT: L 116 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8534 (tmmt) REVERT: M 116 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8549 (tmmt) REVERT: N 50 LYS cc_start: 0.9139 (ttpm) cc_final: 0.8872 (tmmt) REVERT: O 50 LYS cc_start: 0.9138 (ttpm) cc_final: 0.8871 (tmmt) REVERT: P 116 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8545 (tmmt) REVERT: Q 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8877 (tmmt) REVERT: R 50 LYS cc_start: 0.9127 (ttpm) cc_final: 0.8863 (tmmt) REVERT: S 50 LYS cc_start: 0.9129 (ttpm) cc_final: 0.8867 (tmmt) REVERT: T 50 LYS cc_start: 0.9136 (ttpm) cc_final: 0.8871 (tmmt) REVERT: V 50 LYS cc_start: 0.9131 (ttpm) cc_final: 0.8866 (tmmt) REVERT: W 50 LYS cc_start: 0.9140 (ttpm) cc_final: 0.8873 (tmmt) REVERT: X 50 LYS cc_start: 0.9124 (ttpm) cc_final: 0.8863 (tmmt) REVERT: Y 50 LYS cc_start: 0.9123 (ttpm) cc_final: 0.8864 (tmmt) outliers start: 88 outliers final: 24 residues processed: 702 average time/residue: 0.9260 time to fit residues: 746.1513 Evaluate side-chains 625 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 601 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 373 optimal weight: 20.0000 chunk 270 optimal weight: 0.0050 chunk 84 optimal weight: 6.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS B 10 HIS B 133 HIS ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS G 10 HIS G 133 HIS ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 HIS ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 HIS K 10 HIS L 10 HIS L 133 HIS ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 HIS ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 HIS ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 HIS P 10 HIS P 133 HIS Q 10 HIS Q 133 HIS R 10 HIS R 133 HIS S 10 HIS S 133 HIS ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 HIS X 10 HIS X 133 HIS Y 10 HIS Y 133 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.119323 restraints weight = 25156.675| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 0.62 r_work: 0.3117 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2695 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.172 Angle : 0.610 6.037 46728 Z= 0.335 Chirality : 0.041 0.153 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.368 18.931 4512 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.08 % Allowed : 10.69 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.69 (0.13), residues: 4104 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.90 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 60 TYR 0.023 0.003 TYR V 36 PHE 0.025 0.003 PHE L 38 TRP 0.013 0.004 TRP K 90 HIS 0.005 0.001 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00343 (34704) covalent geometry : angle 0.61046 (46728) hydrogen bonds : bond 0.04975 ( 2688) hydrogen bonds : angle 3.61322 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 612 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8934 (tmmt) REVERT: B 116 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8829 (tttm) REVERT: C 50 LYS cc_start: 0.9176 (ttpm) cc_final: 0.8937 (tmmt) REVERT: D 50 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8927 (tmmt) REVERT: E 116 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8828 (tttm) REVERT: F 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8924 (tmmt) REVERT: G 50 LYS cc_start: 0.9144 (ttpm) cc_final: 0.8917 (tmmt) REVERT: H 116 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8824 (tttm) REVERT: I 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8924 (tmmt) REVERT: J 50 LYS cc_start: 0.9177 (ttpm) cc_final: 0.8940 (tmmt) REVERT: L 116 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8826 (tttm) REVERT: M 116 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8826 (tttm) REVERT: N 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8928 (tmmt) REVERT: O 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8929 (tmmt) REVERT: P 116 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8824 (tttm) REVERT: Q 50 LYS cc_start: 0.9176 (ttpm) cc_final: 0.8939 (tmmt) REVERT: R 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8922 (tmmt) REVERT: S 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8929 (tmmt) REVERT: T 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8929 (tmmt) REVERT: V 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8922 (tmmt) REVERT: W 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8928 (tmmt) REVERT: X 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8921 (tmmt) REVERT: Y 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8923 (tmmt) outliers start: 40 outliers final: 26 residues processed: 651 average time/residue: 0.9732 time to fit residues: 720.5275 Evaluate side-chains 610 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 584 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 168 optimal weight: 0.0570 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 overall best weight: 6.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 HIS ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 HIS ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 HIS ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 HIS ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118445 restraints weight = 25148.355| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.62 r_work: 0.3091 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2668 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34704 Z= 0.202 Angle : 0.650 6.213 46728 Z= 0.356 Chirality : 0.043 0.153 4920 Planarity : 0.005 0.039 6144 Dihedral : 4.415 18.482 4512 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 10.04 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.60 (0.13), residues: 4104 helix: 3.54 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.95 (0.27), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 60 TYR 0.024 0.003 TYR N 36 PHE 0.028 0.003 PHE B 38 TRP 0.013 0.004 TRP K 90 HIS 0.006 0.002 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.00406 (34704) covalent geometry : angle 0.64995 (46728) hydrogen bonds : bond 0.05260 ( 2688) hydrogen bonds : angle 3.67302 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 584 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8921 (tmmt) REVERT: C 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8920 (tmmt) REVERT: D 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8914 (tmmt) REVERT: F 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8912 (tmmt) REVERT: G 50 LYS cc_start: 0.9145 (ttpm) cc_final: 0.8907 (tmmt) REVERT: I 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8909 (tmmt) REVERT: J 50 LYS cc_start: 0.9171 (ttpm) cc_final: 0.8925 (tmmt) REVERT: N 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8919 (tmmt) REVERT: O 50 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8917 (tmmt) REVERT: Q 50 LYS cc_start: 0.9172 (ttpm) cc_final: 0.8924 (tmmt) REVERT: R 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8909 (tmmt) REVERT: S 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8917 (tmmt) REVERT: T 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8918 (tmmt) REVERT: V 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8915 (tmmt) REVERT: W 50 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8917 (tmmt) REVERT: X 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8912 (tmmt) REVERT: Y 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8919 (tmmt) outliers start: 49 outliers final: 38 residues processed: 632 average time/residue: 0.9647 time to fit residues: 694.0307 Evaluate side-chains 718 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 680 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 378 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 10 HIS C 10 HIS D 10 HIS E 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS K 10 HIS L 10 HIS M 10 HIS N 10 HIS O 10 HIS P 10 HIS Q 10 HIS R 10 HIS S 10 HIS T 10 HIS V 10 HIS W 10 HIS X 10 HIS Y 10 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.132164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119996 restraints weight = 24925.296| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.63 r_work: 0.3131 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2717 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34704 Z= 0.148 Angle : 0.585 5.838 46728 Z= 0.320 Chirality : 0.040 0.150 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.320 19.413 4512 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 10.15 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.77 (0.13), residues: 4104 helix: 3.70 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.82 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.021 0.002 TYR M 36 PHE 0.022 0.003 PHE B 38 TRP 0.012 0.003 TRP K 90 HIS 0.005 0.001 HIS O 125 Details of bonding type rmsd covalent geometry : bond 0.00290 (34704) covalent geometry : angle 0.58473 (46728) hydrogen bonds : bond 0.04678 ( 2688) hydrogen bonds : angle 3.55919 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 680 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8932 (tmmt) REVERT: B 116 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8649 (tmmt) REVERT: C 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8932 (tmmt) REVERT: D 50 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8927 (tmmt) REVERT: E 116 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8645 (tmmt) REVERT: F 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8922 (tmmt) REVERT: G 50 LYS cc_start: 0.9138 (ttpm) cc_final: 0.8911 (tmmt) REVERT: H 116 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8640 (tmmt) REVERT: I 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8919 (tmmt) REVERT: J 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8933 (tmmt) REVERT: L 116 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8646 (tmmt) REVERT: M 116 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8651 (tmmt) REVERT: N 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8926 (tmmt) REVERT: O 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8923 (tmmt) REVERT: P 116 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8642 (tmmt) REVERT: Q 50 LYS cc_start: 0.9176 (ttpm) cc_final: 0.8935 (tmmt) REVERT: R 50 LYS cc_start: 0.9146 (ttpm) cc_final: 0.8916 (tmmt) REVERT: S 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8926 (tmmt) REVERT: T 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8927 (tmmt) REVERT: V 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8918 (tmmt) REVERT: W 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8928 (tmmt) REVERT: X 50 LYS cc_start: 0.9145 (ttpm) cc_final: 0.8919 (tmmt) REVERT: Y 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8921 (tmmt) outliers start: 48 outliers final: 24 residues processed: 704 average time/residue: 0.9830 time to fit residues: 784.7213 Evaluate side-chains 704 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 680 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 390 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 368 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 10 HIS C 10 HIS D 10 HIS E 10 HIS F 10 HIS G 10 HIS ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS J 10 HIS K 10 HIS L 10 HIS M 10 HIS N 10 HIS O 10 HIS P 10 HIS Q 10 HIS R 10 HIS S 10 HIS T 10 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 HIS X 10 HIS Y 10 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119964 restraints weight = 25036.071| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.63 r_work: 0.3119 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2696 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34704 Z= 0.158 Angle : 0.605 6.441 46728 Z= 0.330 Chirality : 0.040 0.148 4920 Planarity : 0.004 0.030 6144 Dihedral : 4.345 19.181 4512 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 10.71 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.72 (0.13), residues: 4104 helix: 3.66 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.81 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 60 TYR 0.023 0.003 TYR O 36 PHE 0.023 0.003 PHE E 38 TRP 0.012 0.003 TRP Y 90 HIS 0.005 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00313 (34704) covalent geometry : angle 0.60519 (46728) hydrogen bonds : bond 0.04788 ( 2688) hydrogen bonds : angle 3.57312 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 680 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9180 (ttpm) cc_final: 0.8934 (tmmt) REVERT: B 116 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8628 (tmmt) REVERT: C 50 LYS cc_start: 0.9185 (ttpm) cc_final: 0.8937 (tmmt) REVERT: D 50 LYS cc_start: 0.9174 (ttpm) cc_final: 0.8927 (tmmt) REVERT: E 116 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8628 (tmmt) REVERT: F 50 LYS cc_start: 0.9172 (ttpm) cc_final: 0.8926 (tmmt) REVERT: G 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8916 (tmmt) REVERT: H 116 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8628 (tmmt) REVERT: I 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8924 (tmmt) REVERT: J 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8939 (tmmt) REVERT: L 116 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8631 (tmmt) REVERT: M 116 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8633 (tmmt) REVERT: N 50 LYS cc_start: 0.9177 (ttpm) cc_final: 0.8932 (tmmt) REVERT: O 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8929 (tmmt) REVERT: P 116 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8625 (tmmt) REVERT: Q 50 LYS cc_start: 0.9188 (ttpm) cc_final: 0.8940 (tmmt) REVERT: R 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8919 (tmmt) REVERT: S 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8928 (tmmt) REVERT: T 50 LYS cc_start: 0.9178 (ttpm) cc_final: 0.8933 (tmmt) REVERT: V 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8921 (tmmt) REVERT: W 50 LYS cc_start: 0.9176 (ttpm) cc_final: 0.8931 (tmmt) REVERT: X 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8922 (tmmt) REVERT: Y 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8923 (tmmt) outliers start: 24 outliers final: 24 residues processed: 704 average time/residue: 0.9817 time to fit residues: 783.2543 Evaluate side-chains 704 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 680 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 62 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 255 optimal weight: 0.0170 chunk 204 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 10 HIS C 10 HIS D 10 HIS E 10 HIS F 10 HIS G 10 HIS ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS J 10 HIS K 10 HIS L 10 HIS M 10 HIS N 10 HIS O 10 HIS P 10 HIS Q 10 HIS R 10 HIS S 10 HIS T 10 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 HIS X 10 HIS Y 10 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120275 restraints weight = 24869.614| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.62 r_work: 0.3120 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2697 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34704 Z= 0.167 Angle : 0.624 7.268 46728 Z= 0.338 Chirality : 0.041 0.150 4920 Planarity : 0.004 0.031 6144 Dihedral : 4.366 19.012 4512 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 10.58 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.70 (0.13), residues: 4104 helix: 3.64 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.83 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 60 TYR 0.023 0.003 TYR O 36 PHE 0.024 0.003 PHE M 38 TRP 0.012 0.003 TRP B 90 HIS 0.005 0.001 HIS O 125 Details of bonding type rmsd covalent geometry : bond 0.00331 (34704) covalent geometry : angle 0.62374 (46728) hydrogen bonds : bond 0.04890 ( 2688) hydrogen bonds : angle 3.58358 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19739.68 seconds wall clock time: 335 minutes 30.16 seconds (20130.16 seconds total)