Starting phenix.real_space_refine on Mon Jul 6 11:15:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sju_54954/07_2026/9sju_54954_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sju_54954/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9sju_54954/07_2026/9sju_54954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sju_54954/07_2026/9sju_54954.map" model { file = "/net/cci-nas-00/data/ceres_data/9sju_54954/07_2026/9sju_54954_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sju_54954/07_2026/9sju_54954_neut.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 1 Ad-hoc single atom residues: {' FE': 4} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.64, 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: 2.72 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: 0.54 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: 6.01 Time building geometry restraints manager: 3.66 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 2.960 nonbonded pdb="FE FE R 201 " pdb="FE FE R 205 " model vdw 0.005 2.960 nonbonded pdb="FE FE R 204 " pdb="FE FE R 205 " model vdw 0.005 2.960 nonbonded pdb="FE FE F 203 " pdb="FE FE F 204 " model vdw 0.005 2.960 nonbonded pdb="FE FE J 201 " pdb="FE FE J 205 " model vdw 0.006 2.960 ... (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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 24.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 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/Z covalent geometry : bond 0.00341 / 0.17 (34704) covalent geometry : angle 0.60818 / 0.33 (46728) hydrogen bonds : bond 0.07540 / 5.10 ( 2688) hydrogen bonds : angle 3.80432 / 2.74 ( 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 : 1.313 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: 0.9450 time to fit residues: 766.1295 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 : 1.442 ------------------------------------------------------------------------------- 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... 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 = 0.3428 r_free = 0.3428 target = 0.133479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121406 restraints weight = 25000.638| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.62 r_work: 0.3136 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2714 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34704 Z= 0.163 Angle : 0.612 5.997 46728 Z= 0.334 Chirality : 0.041 0.258 4920 Planarity : 0.005 0.045 6144 Dihedral : 7.619 57.092 4652 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.11 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: 4.74 (0.13), residues: 4104 helix: 3.64 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.01 (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 P 36 PHE 0.025 0.003 PHE A 38 TRP 0.011 0.003 TRP H 90 HIS 0.009 0.002 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (34704) covalent geometry : angle 0.61249 / 0.33 (46728) hydrogen bonds : bond 0.04843 / 3.28 ( 2688) hydrogen bonds : angle 3.60484 / 2.59 ( 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 580 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.425 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: I 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8932 (tmmt) REVERT: V 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8926 (tmmt) REVERT: X 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8927 (tmmt) REVERT: Y 50 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8931 (tmmt) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.9226 time to fit residues: 614.2359 Evaluate side-chains 583 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 20.0000 chunk 364 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 72 GLN ** 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** 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** N 72 GLN ** 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** R 72 GLN ** 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** X 72 GLN ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117665 restraints weight = 24959.788| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.63 r_work: 0.3095 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2673 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.0812 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= 0.228 Angle : 0.688 6.414 46728 Z= 0.376 Chirality : 0.045 0.259 4920 Planarity : 0.006 0.045 6144 Dihedral : 4.449 18.206 4512 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.54 % Allowed : 9.85 % 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: 4.52 (0.13), residues: 4104 helix: 3.47 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.00 (0.27), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 153 TYR 0.026 0.003 TYR X 36 PHE 0.031 0.004 PHE W 38 TRP 0.014 0.004 TRP M 90 HIS 0.006 0.002 HIS K 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (34704) covalent geometry : angle 0.68781 / 0.38 (46728) hydrogen bonds : bond 0.05460 / 3.70 ( 2688) hydrogen bonds : angle 3.71139 / 2.67 ( 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 647 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 627 time to evaluate : 1.184 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: 0.9170 (ttpm) cc_final: 0.8921 (tmmt) REVERT: C 50 LYS cc_start: 0.9174 (ttpm) cc_final: 0.8920 (tmmt) REVERT: D 50 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8911 (tmmt) REVERT: F 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8911 (tmmt) REVERT: G 50 LYS cc_start: 0.9146 (ttpm) cc_final: 0.8905 (tmmt) REVERT: I 50 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8913 (tmmt) REVERT: J 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8918 (tmmt) REVERT: N 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8918 (tmmt) REVERT: O 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8914 (tmmt) REVERT: Q 50 LYS cc_start: 0.9179 (ttpm) cc_final: 0.8924 (tmmt) REVERT: R 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8907 (tmmt) REVERT: S 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8912 (tmmt) REVERT: T 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8913 (tmmt) REVERT: V 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8908 (tmmt) REVERT: W 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8913 (tmmt) REVERT: X 50 LYS cc_start: 0.9144 (ttpm) cc_final: 0.8904 (tmmt) REVERT: Y 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8907 (tmmt) outliers start: 20 outliers final: 20 residues processed: 647 average time/residue: 0.9056 time to fit residues: 673.1888 Evaluate side-chains 647 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 627 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 M residue 164 GLU Chi-restraints excluded: chain N 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: 5.9990 chunk 51 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN B 10 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118682 restraints weight = 24946.359| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.63 r_work: 0.3105 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2683 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34704 Z= 0.179 Angle : 0.620 6.080 46728 Z= 0.339 Chirality : 0.042 0.158 4920 Planarity : 0.005 0.036 6144 Dihedral : 4.370 18.609 4512 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.03 % Allowed : 9.60 % Favored : 89.37 % 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: 4.66 (0.13), residues: 4104 helix: 3.59 (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 L 153 TYR 0.024 0.003 TYR F 36 PHE 0.026 0.003 PHE F 38 TRP 0.013 0.004 TRP T 90 HIS 0.005 0.001 HIS O 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (34704) covalent geometry : angle 0.61982 / 0.34 (46728) hydrogen bonds : bond 0.05033 / 3.41 ( 2688) hydrogen bonds : angle 3.62578 / 2.61 ( 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 658 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 620 time to evaluate : 1.458 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: A 50 LYS cc_start: 0.9181 (ttpm) cc_final: 0.8938 (tmmt) REVERT: B 116 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8821 (tttm) REVERT: C 50 LYS cc_start: 0.9184 (ttpm) cc_final: 0.8934 (tmmt) REVERT: D 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8925 (tmmt) REVERT: E 116 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8821 (tttm) REVERT: F 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8925 (tmmt) REVERT: G 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8920 (tmmt) REVERT: H 116 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8824 (tttm) REVERT: I 50 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8923 (tmmt) REVERT: J 50 LYS cc_start: 0.9178 (ttpm) cc_final: 0.8935 (tmmt) REVERT: K 116 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8824 (tttm) REVERT: L 116 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8823 (tttm) REVERT: M 116 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8831 (tttm) REVERT: N 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8929 (tmmt) REVERT: O 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8925 (tmmt) REVERT: P 116 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8825 (tttm) REVERT: Q 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8935 (tmmt) REVERT: R 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8922 (tmmt) REVERT: S 50 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8925 (tmmt) REVERT: T 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8925 (tmmt) REVERT: V 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8923 (tmmt) REVERT: W 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8928 (tmmt) REVERT: X 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8919 (tmmt) REVERT: Y 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8920 (tmmt) outliers start: 38 outliers final: 4 residues processed: 658 average time/residue: 0.8644 time to fit residues: 655.3498 Evaluate side-chains 611 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 607 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 367 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 382 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 HIS A 133 HIS ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 133 HIS ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 133 HIS ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS D 133 HIS ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS E 133 HIS ** F 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 133 HIS ** G 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 133 HIS ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS J 72 GLN J 133 HIS ** K 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 HIS ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS L 133 HIS ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS 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 57 HIS O 133 HIS ** P 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 HIS P 133 HIS ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 HIS Q 133 HIS ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS R 133 HIS ** S 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS S 133 HIS ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 HIS T 133 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 57 HIS V 133 HIS ** W 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 HIS W 133 HIS ** X 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 HIS X 133 HIS ** Y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS Y 133 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117611 restraints weight = 25125.783| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.62 r_work: 0.3119 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.2709 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.0865 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= 0.197 Angle : 0.637 6.188 46728 Z= 0.350 Chirality : 0.043 0.153 4920 Planarity : 0.005 0.039 6144 Dihedral : 4.412 18.560 4512 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.68 % Allowed : 9.42 % Favored : 88.91 % 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: 4.59 (0.13), residues: 4104 helix: 3.53 (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 F 153 TYR 0.024 0.003 TYR Q 36 PHE 0.028 0.003 PHE W 38 TRP 0.013 0.004 TRP K 90 HIS 0.006 0.002 HIS K 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (34704) covalent geometry : angle 0.63742 / 0.35 (46728) hydrogen bonds : bond 0.05210 / 3.53 ( 2688) hydrogen bonds : angle 3.65518 / 2.63 ( 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 656 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 594 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8904 (tmmt) REVERT: C 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8900 (tmmt) REVERT: D 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8899 (tmmt) REVERT: E 116 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8751 (tttm) REVERT: F 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8890 (tmmt) REVERT: G 50 LYS cc_start: 0.9144 (ttpm) cc_final: 0.8888 (tmmt) REVERT: I 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8895 (tmmt) REVERT: J 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8901 (tmmt) REVERT: K 116 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8755 (tttm) REVERT: M 116 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8770 (tttm) REVERT: N 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8901 (tmmt) REVERT: O 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8894 (tmmt) REVERT: Q 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8905 (tmmt) REVERT: R 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8887 (tmmt) REVERT: S 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8895 (tmmt) REVERT: T 50 LYS cc_start: 0.9149 (ttpm) cc_final: 0.8889 (tmmt) REVERT: V 50 LYS cc_start: 0.9139 (ttpm) cc_final: 0.8883 (tmmt) REVERT: W 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8894 (tmmt) REVERT: X 50 LYS cc_start: 0.9145 (ttpm) cc_final: 0.8896 (tmmt) REVERT: Y 50 LYS cc_start: 0.9137 (ttpm) cc_final: 0.8882 (tmmt) outliers start: 62 outliers final: 24 residues processed: 656 average time/residue: 0.8997 time to fit residues: 677.1961 Evaluate side-chains 622 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 598 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 5.9990 chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 G 10 HIS ** 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 ** 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 ** R 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 HIS ** 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** W 72 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117544 restraints weight = 25097.681| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.63 r_work: 0.3120 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work: 0.2710 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.0868 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= 0.197 Angle : 0.637 6.173 46728 Z= 0.350 Chirality : 0.043 0.154 4920 Planarity : 0.005 0.038 6144 Dihedral : 4.396 18.559 4512 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.22 % Allowed : 9.69 % Favored : 89.10 % 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 : 0.96 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 60 TYR 0.024 0.003 TYR J 36 PHE 0.027 0.003 PHE F 38 TRP 0.013 0.004 TRP D 90 HIS 0.006 0.001 HIS X 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (34704) covalent geometry : angle 0.63712 / 0.35 (46728) hydrogen bonds : bond 0.05196 / 3.52 ( 2688) hydrogen bonds : angle 3.65248 / 2.62 ( 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 643 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 598 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8905 (tmmt) REVERT: B 116 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8567 (tmmt) REVERT: C 50 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8904 (tmmt) REVERT: D 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8897 (tmmt) REVERT: F 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8895 (tmmt) REVERT: G 50 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8894 (tmmt) REVERT: H 116 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8552 (tmmt) REVERT: I 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8895 (tmmt) REVERT: J 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8905 (tmmt) REVERT: L 116 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8554 (tmmt) REVERT: N 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8903 (tmmt) REVERT: O 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8895 (tmmt) REVERT: P 116 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8556 (tmmt) REVERT: Q 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8909 (tmmt) REVERT: R 50 LYS cc_start: 0.9151 (ttpm) cc_final: 0.8893 (tmmt) REVERT: S 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8903 (tmmt) REVERT: T 50 LYS cc_start: 0.9156 (ttpm) cc_final: 0.8899 (tmmt) REVERT: V 50 LYS cc_start: 0.9144 (ttpm) cc_final: 0.8894 (tmmt) REVERT: W 50 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8898 (tmmt) REVERT: X 50 LYS cc_start: 0.9149 (ttpm) cc_final: 0.8898 (tmmt) REVERT: Y 50 LYS cc_start: 0.9135 (ttpm) cc_final: 0.8882 (tmmt) outliers start: 45 outliers final: 26 residues processed: 643 average time/residue: 0.9476 time to fit residues: 698.0026 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 : 1.229 ------------------------------------------------------------------------------- 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 88 ASP 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 88 ASP 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: 5.9990 chunk 311 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 270 optimal weight: 0.0170 chunk 84 optimal weight: 7.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS B 10 HIS ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS E 10 HIS F 10 HIS G 10 HIS H 10 HIS ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS K 10 HIS L 10 HIS M 10 HIS N 10 HIS ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 HIS Q 10 HIS R 10 HIS S 10 HIS ** T 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 10 HIS W 10 HIS X 10 HIS Y 10 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.119421 restraints weight = 25246.681| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 0.63 r_work: 0.3143 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.2737 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.0882 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 : 0.575 5.828 46728 Z= 0.315 Chirality : 0.040 0.149 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.314 19.402 4512 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 9.17 % Favored : 88.91 % 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: 3.75 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.72 (0.25), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 60 TYR 0.021 0.002 TYR D 36 PHE 0.022 0.003 PHE M 38 TRP 0.011 0.003 TRP E 90 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (34704) covalent geometry : angle 0.57505 / 0.31 (46728) hydrogen bonds : bond 0.04668 / 3.16 ( 2688) hydrogen bonds : angle 3.55206 / 2.55 ( 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 701 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 630 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8904 (tmmt) REVERT: B 116 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8765 (tttm) REVERT: C 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8905 (tmmt) REVERT: D 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8894 (tmmt) REVERT: E 116 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8563 (tmmt) REVERT: F 50 LYS cc_start: 0.9145 (ttpm) cc_final: 0.8887 (tmmt) REVERT: G 50 LYS cc_start: 0.9143 (ttpm) cc_final: 0.8892 (tmmt) REVERT: H 116 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8752 (tttm) REVERT: I 50 LYS cc_start: 0.9149 (ttpm) cc_final: 0.8890 (tmmt) REVERT: J 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8896 (tmmt) REVERT: K 116 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8558 (tmmt) REVERT: L 116 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8752 (tttm) REVERT: M 116 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8581 (tmmt) REVERT: N 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8896 (tmmt) REVERT: O 50 LYS cc_start: 0.9141 (ttpm) cc_final: 0.8887 (tmmt) REVERT: P 116 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8758 (tttm) REVERT: Q 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8906 (tmmt) REVERT: R 50 LYS cc_start: 0.9139 (ttpm) cc_final: 0.8888 (tmmt) REVERT: S 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8900 (tmmt) REVERT: T 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8894 (tmmt) REVERT: V 50 LYS cc_start: 0.9134 (ttpm) cc_final: 0.8885 (tmmt) REVERT: W 50 LYS cc_start: 0.9152 (ttpm) cc_final: 0.8896 (tmmt) REVERT: X 50 LYS cc_start: 0.9134 (ttpm) cc_final: 0.8884 (tmmt) REVERT: Y 50 LYS cc_start: 0.9134 (ttpm) cc_final: 0.8881 (tmmt) outliers start: 71 outliers final: 4 residues processed: 701 average time/residue: 0.8736 time to fit residues: 707.2700 Evaluate side-chains 697 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 693 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain P 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: 3.9990 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: 10.0000 chunk 313 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN 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** K 133 HIS ** 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 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 72 GLN 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 72 GLN Y 133 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117779 restraints weight = 25226.767| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 0.63 r_work: 0.3144 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.2743 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.2743 ------------------------------------------------------------------------------- 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: 18 | |-----------------------------------------------------------------------------| |-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: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0902 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= 0.223 Angle : 0.672 6.291 46728 Z= 0.368 Chirality : 0.044 0.154 4920 Planarity : 0.005 0.042 6144 Dihedral : 4.444 18.214 4512 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.11 % Allowed : 10.39 % Favored : 88.50 % 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: 4.59 (0.13), residues: 4104 helix: 3.53 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.98 (0.27), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 60 TYR 0.025 0.003 TYR X 36 PHE 0.029 0.004 PHE F 38 TRP 0.014 0.004 TRP T 90 HIS 0.007 0.002 HIS P 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (34704) covalent geometry : angle 0.67177 / 0.37 (46728) hydrogen bonds : bond 0.05395 / 3.66 ( 2688) hydrogen bonds : angle 3.69653 / 2.66 ( 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 625 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 584 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9146 (ttpm) cc_final: 0.8884 (tmmt) REVERT: C 50 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8884 (tmmt) REVERT: D 50 LYS cc_start: 0.9144 (ttpm) cc_final: 0.8878 (tmmt) REVERT: E 116 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8743 (tttm) REVERT: F 50 LYS cc_start: 0.9139 (ttpm) cc_final: 0.8873 (tmmt) REVERT: G 50 LYS cc_start: 0.9133 (ttpm) cc_final: 0.8874 (tmmt) REVERT: I 50 LYS cc_start: 0.9141 (ttpm) cc_final: 0.8877 (tmmt) REVERT: J 50 LYS cc_start: 0.9154 (ttpm) cc_final: 0.8886 (tmmt) REVERT: K 116 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8742 (tttm) REVERT: M 116 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8758 (tttm) REVERT: N 50 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8877 (tmmt) REVERT: O 50 LYS cc_start: 0.9134 (ttpm) cc_final: 0.8872 (tmmt) REVERT: Q 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8888 (tmmt) REVERT: R 50 LYS cc_start: 0.9131 (ttpm) cc_final: 0.8870 (tmmt) REVERT: S 50 LYS cc_start: 0.9149 (ttpm) cc_final: 0.8886 (tmmt) REVERT: T 50 LYS cc_start: 0.9140 (ttpm) cc_final: 0.8877 (tmmt) REVERT: V 50 LYS cc_start: 0.9131 (ttpm) cc_final: 0.8871 (tmmt) REVERT: W 50 LYS cc_start: 0.9143 (ttpm) cc_final: 0.8879 (tmmt) REVERT: X 50 LYS cc_start: 0.9136 (ttpm) cc_final: 0.8886 (tmmt) REVERT: Y 50 LYS cc_start: 0.9128 (ttpm) cc_final: 0.8865 (tmmt) outliers start: 41 outliers final: 3 residues processed: 625 average time/residue: 0.9965 time to fit residues: 712.5349 Evaluate side-chains 683 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 680 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain X residue 88 ASP 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: 0.9980 chunk 318 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 378 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3406 r_free = 0.3406 target = 0.131937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119932 restraints weight = 24951.707| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.62 r_work: 0.3133 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2718 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.0908 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= 0.137 Angle : 0.563 5.694 46728 Z= 0.308 Chirality : 0.039 0.148 4920 Planarity : 0.004 0.025 6144 Dihedral : 4.292 19.681 4512 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.22 % Allowed : 11.34 % Favored : 88.45 % 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: 4.85 (0.13), residues: 4104 helix: 3.81 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.72 (0.25), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 60 TYR 0.020 0.002 TYR M 36 PHE 0.020 0.002 PHE W 38 TRP 0.011 0.003 TRP D 90 HIS 0.005 0.001 HIS V 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (34704) covalent geometry : angle 0.56302 / 0.31 (46728) hydrogen bonds : bond 0.04471 / 3.03 ( 2688) hydrogen bonds : angle 3.51833 / 2.53 ( 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 706 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 698 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9179 (ttpm) cc_final: 0.8935 (tmmt) REVERT: B 116 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8650 (tmmt) REVERT: C 50 LYS cc_start: 0.9185 (ttpm) cc_final: 0.8935 (tmmt) REVERT: D 50 LYS cc_start: 0.9174 (ttpm) cc_final: 0.8928 (tmmt) REVERT: E 116 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8819 (tttm) REVERT: F 50 LYS cc_start: 0.9171 (ttpm) cc_final: 0.8924 (tmmt) REVERT: G 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8920 (tmmt) REVERT: H 116 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8643 (tmmt) REVERT: I 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8925 (tmmt) REVERT: J 50 LYS cc_start: 0.9182 (ttpm) cc_final: 0.8934 (tmmt) REVERT: K 116 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8824 (tttm) REVERT: L 116 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8634 (tmmt) REVERT: M 116 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8845 (tttm) REVERT: N 50 LYS cc_start: 0.9173 (ttpm) cc_final: 0.8927 (tmmt) REVERT: O 50 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8920 (tmmt) REVERT: P 116 LYS cc_start: 0.9076 (ttmm) cc_final: 0.8642 (tmmt) REVERT: Q 50 LYS cc_start: 0.9185 (ttpm) cc_final: 0.8937 (tmmt) REVERT: R 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8918 (tmmt) REVERT: S 50 LYS cc_start: 0.9169 (ttpm) cc_final: 0.8929 (tmmt) REVERT: T 50 LYS cc_start: 0.9166 (ttpm) cc_final: 0.8925 (tmmt) REVERT: V 50 LYS cc_start: 0.9148 (ttpm) cc_final: 0.8911 (tmmt) REVERT: W 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8928 (tmmt) REVERT: X 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8913 (tmmt) REVERT: Y 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8913 (tmmt) outliers start: 8 outliers final: 2 residues processed: 703 average time/residue: 1.0349 time to fit residues: 829.0410 Evaluate side-chains 697 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 695 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain K 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: 4.9990 chunk 362 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS B 10 HIS C 10 HIS D 10 HIS E 10 HIS F 10 HIS G 10 HIS G 133 HIS ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS K 10 HIS L 10 HIS M 10 HIS N 10 HIS ** O 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118712 restraints weight = 25122.697| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.63 r_work: 0.3115 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work: 0.2702 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2702 ------------------------------------------------------------------------------- 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: 18 | |-----------------------------------------------------------------------------| |-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: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34704 Z= 0.178 Angle : 0.628 6.564 46728 Z= 0.342 Chirality : 0.042 0.148 4920 Planarity : 0.004 0.034 6144 Dihedral : 4.367 18.784 4512 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.78 % Allowed : 10.36 % Favored : 88.85 % 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: 3.63 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.88 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 60 TYR 0.022 0.003 TYR D 36 PHE 0.025 0.003 PHE F 38 TRP 0.013 0.004 TRP D 90 HIS 0.005 0.001 HIS K 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (34704) covalent geometry : angle 0.62767 / 0.34 (46728) hydrogen bonds : bond 0.04970 / 3.37 ( 2688) hydrogen bonds : angle 3.59980 / 2.58 ( 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 708 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 679 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8905 (tmmt) REVERT: B 116 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8560 (tmmt) REVERT: C 50 LYS cc_start: 0.9174 (ttpm) cc_final: 0.8906 (tmmt) REVERT: D 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8901 (tmmt) REVERT: E 116 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8743 (tttm) REVERT: F 50 LYS cc_start: 0.9155 (ttpm) cc_final: 0.8891 (tmmt) REVERT: G 50 LYS cc_start: 0.9150 (ttpm) cc_final: 0.8896 (tmmt) REVERT: H 116 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8554 (tmmt) REVERT: I 50 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8898 (tmmt) REVERT: J 50 LYS cc_start: 0.9170 (ttpm) cc_final: 0.8907 (tmmt) REVERT: K 116 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8753 (tttm) REVERT: L 116 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8551 (tmmt) REVERT: M 116 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8766 (tttm) REVERT: N 50 LYS cc_start: 0.9167 (ttpm) cc_final: 0.8901 (tmmt) REVERT: O 50 LYS cc_start: 0.9149 (ttpm) cc_final: 0.8891 (tmmt) REVERT: P 116 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8555 (tmmt) REVERT: Q 50 LYS cc_start: 0.9176 (ttpm) cc_final: 0.8909 (tmmt) REVERT: R 50 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8891 (tmmt) REVERT: S 50 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8903 (tmmt) REVERT: T 50 LYS cc_start: 0.9159 (ttpm) cc_final: 0.8898 (tmmt) REVERT: V 50 LYS cc_start: 0.9142 (ttpm) cc_final: 0.8890 (tmmt) REVERT: W 50 LYS cc_start: 0.9162 (ttpm) cc_final: 0.8901 (tmmt) REVERT: X 50 LYS cc_start: 0.9146 (ttpm) cc_final: 0.8891 (tmmt) REVERT: Y 50 LYS cc_start: 0.9142 (ttpm) cc_final: 0.8885 (tmmt) outliers start: 29 outliers final: 26 residues processed: 684 average time/residue: 0.9939 time to fit residues: 774.8683 Evaluate side-chains 705 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 679 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 88 ASP Chi-restraints excluded: chain L residue 164 GLU 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 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 88 ASP Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU 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: 5.9990 chunk 255 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118550 restraints weight = 24914.052| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.62 r_work: 0.3120 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work: 0.2707 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.2707 ------------------------------------------------------------------------------- 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: 18 | |-----------------------------------------------------------------------------| |-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: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.0899 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= 0.175 Angle : 0.630 6.443 46728 Z= 0.343 Chirality : 0.042 0.151 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.372 18.906 4512 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.73 % Allowed : 10.66 % Favored : 88.61 % 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: 3.63 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.87 (0.26), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 60 TYR 0.023 0.003 TYR D 36 PHE 0.025 0.003 PHE F 38 TRP 0.012 0.003 TRP L 90 HIS 0.005 0.001 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (34704) covalent geometry : angle 0.63000 / 0.34 (46728) hydrogen bonds : bond 0.04956 / 3.36 ( 2688) hydrogen bonds : angle 3.58700 / 2.57 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18729.44 seconds wall clock time: 318 minutes 53.07 seconds (19133.07 seconds total)