Starting phenix.real_space_refine on Mon Jul 6 15:10:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205.map" model { file = "/net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sht_10205/07_2026/6sht_10205_neut.cif" } resolution = 2.73 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= 0.001 sd= 0.015 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 192 5.16 5 C 22296 2.51 5 N 6264 2.21 5 O 8352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s 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: 37152 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Conformer: "B" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} bond proxies already assigned to first conformer: 1397 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 73 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 72} Link IDs: {None: 72} Chain breaks: 1 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb=" O HOH A 359 " occ=0.33 residue: pdb="FE FE B 201 " occ=0.25 residue: pdb=" O HOH B 359 " occ=0.33 residue: pdb="FE FE C 201 " occ=0.25 residue: pdb=" O HOH C 359 " occ=0.33 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb=" O HOH D 359 " occ=0.33 residue: pdb="FE FE E 201 " occ=0.25 residue: pdb=" O HOH E 359 " occ=0.33 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb=" O HOH F 359 " occ=0.33 ... (remaining 36 not shown) Time building chain proxies: 4.71, per 1000 atoms: 0.13 Number of scatterers: 37152 At special positions: 0 Unit cell: (135.36, 135.36, 135.36, 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 192 16.00 Mg 24 11.99 O 8352 8.00 N 6264 7.00 C 22296 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: 2.90 Conformation dependent library (CDL) restraints added in 2.9 seconds 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 120 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 40 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 120 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 40 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 120 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 40 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 120 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 40 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 120 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 40 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 120 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 40 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 120 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR G 165 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 40 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 120 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR H 165 " --> pdb=" O GLY H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 40 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 120 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 40 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 120 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 40 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 120 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR K 165 " --> pdb=" O GLY K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 40 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 120 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR L 165 " --> pdb=" O GLY L 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 40 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 120 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR M 165 " --> pdb=" O GLY M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 40 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 120 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR N 165 " --> pdb=" O GLY N 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 40 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 120 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR O 165 " --> pdb=" O GLY O 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 40 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 120 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR P 165 " --> pdb=" O GLY P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 40 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 120 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR Q 165 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 120 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR R 165 " --> pdb=" O GLY R 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 40 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 120 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR S 165 " --> pdb=" O GLY S 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 40 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 120 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR T 165 " --> pdb=" O GLY T 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 40 Processing helix chain 'U' and resid 45 through 73 Processing helix chain 'U' and resid 92 through 120 Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR U 165 " --> pdb=" O GLY U 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 40 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 120 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR V 165 " --> pdb=" O GLY V 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 40 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 120 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR W 165 " --> pdb=" O GLY W 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 40 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 120 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9888 1.33 - 1.46: 8088 1.46 - 1.58: 17976 1.58 - 1.71: 48 1.71 - 1.84: 312 Bond restraints: 36312 Sorted by residual: bond pdb=" CA ALA D 157 " pdb=" CB ALA D 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA M 157 " pdb=" CB ALA M 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA B 157 " pdb=" CB ALA B 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA E 157 " pdb=" CB ALA E 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA K 157 " pdb=" CB ALA K 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 ... (remaining 36307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 42168 2.15 - 4.30: 5880 4.30 - 6.44: 888 6.44 - 8.59: 144 8.59 - 10.74: 24 Bond angle restraints: 49104 Sorted by residual: angle pdb=" N HIS B 170 " pdb=" CA HIS B 170 " pdb=" C HIS B 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS D 170 " pdb=" CA HIS D 170 " pdb=" C HIS D 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS Q 170 " pdb=" CA HIS Q 170 " pdb=" C HIS Q 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS U 170 " pdb=" CA HIS U 170 " pdb=" C HIS U 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS J 170 " pdb=" CA HIS J 170 " pdb=" C HIS J 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 ... (remaining 49099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21504 35.95 - 71.90: 1032 71.90 - 107.85: 24 107.85 - 143.80: 0 143.80 - 179.75: 24 Dihedral angle restraints: 22584 sinusoidal: 9456 harmonic: 13128 Sorted by residual: dihedral pdb=" CD BARG A 60 " pdb=" NE BARG A 60 " pdb=" CZ BARG A 60 " pdb=" NH1BARG A 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 60 " pdb=" NE BARG C 60 " pdb=" CZ BARG C 60 " pdb=" NH1BARG C 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 60 " pdb=" NE BARG D 60 " pdb=" CZ BARG D 60 " pdb=" NH1BARG D 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 22581 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.054: 2664 0.054 - 0.105: 1848 0.105 - 0.157: 504 0.157 - 0.209: 72 0.209 - 0.261: 24 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA VAL I 43 " pdb=" N VAL I 43 " pdb=" C VAL I 43 " pdb=" CB VAL I 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL C 43 " pdb=" N VAL C 43 " pdb=" C VAL C 43 " pdb=" CB VAL C 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL K 43 " pdb=" N VAL K 43 " pdb=" C VAL K 43 " pdb=" CB VAL K 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5109 not shown) Planarity restraints: 6480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR F 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR F 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR L 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR L 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR G 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR G 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR G 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 134 " -0.018 2.00e-02 2.50e+03 ... (remaining 6477 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 60 0.98 - 1.96: 48 1.96 - 2.94: 16140 2.94 - 3.92: 107076 3.92 - 4.90: 208788 Warning: very small nonbonded interaction distances. Nonbonded interactions: 332112 Sorted by model distance: nonbonded pdb="FE FE D 201 " pdb="FE FE J 201 " model vdw 0.000 2.960 nonbonded pdb="FE FE D 201 " pdb="FE FE M 201 " model vdw 0.000 2.960 nonbonded pdb="FE FE D 201 " pdb="FE FE V 201 " model vdw 0.000 2.960 nonbonded pdb="FE FE J 201 " pdb="FE FE M 201 " model vdw 0.000 2.960 nonbonded pdb="FE FE J 201 " pdb="FE FE V 201 " model vdw 0.000 2.960 ... (remaining 332107 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=0.00 max=1.00 mean=0.93 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: 1.580 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.750 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 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 : 0.015 0.083 36312 Z= 0.882 Angle : 1.547 10.740 49104 Z= 1.010 Chirality : 0.070 0.261 5112 Planarity : 0.007 0.040 6480 Dihedral : 19.276 179.750 14184 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 13.58 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.11), residues: 4320 helix: -1.81 (0.07), residues: 3384 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG E 40 TYR 0.038 0.007 TYR D 134 PHE 0.034 0.009 PHE T 48 TRP 0.010 0.005 TRP S 90 HIS 0.007 0.003 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.01539 / 0.88 (36312) covalent geometry : angle 1.54698 / 1.01 (49104) hydrogen bonds : bond 0.24973 / 16.53 ( 2640) hydrogen bonds : angle 7.00923 / 5.12 ( 7776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1344 time to evaluate : 1.263 Fit side-chains REVERT: A 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: A 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: A 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: B 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: B 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: B 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: C 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: C 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: C 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: D 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: D 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: D 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: E 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: E 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: E 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: F 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: F 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: F 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: G 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: G 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: G 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: H 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: H 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: H 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: I 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: I 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: I 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: J 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: J 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: J 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: K 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: K 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: K 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: L 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: L 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: L 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: M 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: M 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: M 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: N 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: N 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: N 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: O 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: O 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: O 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: P 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: P 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: P 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: Q 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: Q 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: Q 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: R 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: R 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: R 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: S 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: S 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: S 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: T 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: T 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: T 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: U 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: U 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: U 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: V 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: V 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: V 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: W 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: W 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: W 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: X 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: X 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: X 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) outliers start: 192 outliers final: 24 residues processed: 1392 average time/residue: 0.8143 time to fit residues: 1322.6439 Evaluate side-chains 1026 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 978 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 131 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 131 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain V residue 131 GLU Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain X residue 131 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.0270 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS B 72 GLN B 95 ASN C 22 ASN C 72 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS F 62 HIS F 72 GLN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 57 HIS G 72 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 72 GLN I 72 GLN K 72 GLN K 95 ASN L 22 ASN L 72 GLN M 22 ASN M 55 GLN M 95 ASN M 108 ASN N 8 ASN N 57 HIS ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 72 GLN Q 72 GLN R 72 GLN R 95 ASN ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS S 72 GLN T 55 GLN T 57 HIS T 72 GLN U 57 HIS U 72 GLN U 151 ASN V 8 ASN V 72 GLN W 22 ASN W 57 HIS W 95 ASN X 72 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.077482 restraints weight = 235102.170| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.45 r_work: 0.2413 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (16 function evaluations) r_final: 0.2381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.211 36312 Z= 0.428 Angle : 1.833 41.167 49104 Z= 0.927 Chirality : 0.071 0.661 5112 Planarity : 0.016 0.167 6480 Dihedral : 14.685 179.726 5136 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.90 % Favored : 95.52 % Rotamer: Outliers : 7.00 % Allowed : 18.78 % Favored : 74.23 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.45 (0.11), residues: 4320 helix: -0.62 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.004 ARG R 87 TYR 0.135 0.010 TYR J 31 PHE 0.090 0.007 PHE N 52 TRP 0.082 0.009 TRP D 90 HIS 0.075 0.008 HIS P 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.43 (36312) covalent geometry : angle 1.83266 / 0.93 (49104) hydrogen bonds : bond 0.12705 / 8.48 ( 2640) hydrogen bonds : angle 5.49593 / 3.99 ( 7776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 1173 time to evaluate : 1.201 Fit side-chains REVERT: A 76 ARG cc_start: 0.8740 (mmt-90) cc_final: 0.8497 (mmt180) REVERT: A 138 GLN cc_start: 0.9162 (tp40) cc_final: 0.8938 (tp-100) REVERT: B 138 GLN cc_start: 0.9107 (tp40) cc_final: 0.8830 (tp-100) REVERT: C 76 ARG cc_start: 0.8702 (mmt-90) cc_final: 0.8473 (mmt180) REVERT: C 138 GLN cc_start: 0.9224 (tp40) cc_final: 0.8964 (mm-40) REVERT: D 8 ASN cc_start: 0.8912 (t0) cc_final: 0.8453 (t0) REVERT: D 76 ARG cc_start: 0.8717 (mmt-90) cc_final: 0.8486 (mmt-90) REVERT: E 76 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8316 (mmt180) REVERT: G 14 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: G 138 GLN cc_start: 0.9191 (tp40) cc_final: 0.8969 (tp-100) REVERT: H 41 ASP cc_start: 0.8712 (p0) cc_final: 0.7997 (p0) REVERT: H 76 ARG cc_start: 0.8733 (mmt-90) cc_final: 0.8319 (mmt180) REVERT: I 46 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8271 (ttmm) REVERT: I 65 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8265 (mttm) REVERT: I 76 ARG cc_start: 0.8839 (mmt-90) cc_final: 0.8468 (mmt-90) REVERT: I 138 GLN cc_start: 0.9110 (tp40) cc_final: 0.8898 (tp-100) REVERT: J 46 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7855 (ttmt) REVERT: J 141 SER cc_start: 0.8924 (m) cc_final: 0.8709 (m) REVERT: K 81 ASP cc_start: 0.8262 (m-30) cc_final: 0.7928 (m-30) REVERT: K 138 GLN cc_start: 0.9268 (tp40) cc_final: 0.9014 (tp-100) REVERT: L 8 ASN cc_start: 0.8798 (t0) cc_final: 0.8503 (t0) REVERT: L 76 ARG cc_start: 0.8703 (mmt-90) cc_final: 0.8373 (mmt-90) REVERT: M 46 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8096 (ttmt) REVERT: M 76 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8413 (mmt180) REVERT: M 91 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: M 141 SER cc_start: 0.8858 (m) cc_final: 0.8650 (m) REVERT: N 6 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8913 (ttt180) REVERT: N 76 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8330 (mpt180) REVERT: N 138 GLN cc_start: 0.9119 (tp40) cc_final: 0.8913 (tp-100) REVERT: O 8 ASN cc_start: 0.8871 (t0) cc_final: 0.8526 (t0) REVERT: O 19 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7945 (mtt90) REVERT: O 46 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7783 (ttmt) REVERT: O 91 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: O 138 GLN cc_start: 0.9174 (tp40) cc_final: 0.8957 (tp-100) REVERT: O 141 SER cc_start: 0.8854 (m) cc_final: 0.8605 (m) REVERT: P 76 ARG cc_start: 0.8800 (mmt-90) cc_final: 0.8471 (mmt-90) REVERT: P 138 GLN cc_start: 0.9096 (tp40) cc_final: 0.8885 (tp-100) REVERT: R 42 ASP cc_start: 0.8876 (p0) cc_final: 0.8643 (p0) REVERT: R 46 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8021 (ttmt) REVERT: R 78 PHE cc_start: 0.8867 (m-80) cc_final: 0.8586 (m-80) REVERT: R 81 ASP cc_start: 0.8285 (m-30) cc_final: 0.7986 (m-30) REVERT: S 19 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8136 (mtm110) REVERT: S 76 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8159 (mpt180) REVERT: T 46 LYS cc_start: 0.8158 (ttpp) cc_final: 0.7851 (ttmt) REVERT: U 46 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8396 (ttmm) REVERT: U 138 GLN cc_start: 0.9063 (tp40) cc_final: 0.8797 (tp-100) REVERT: U 141 SER cc_start: 0.8673 (m) cc_final: 0.8434 (m) REVERT: V 6 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8907 (ttt180) REVERT: V 76 ARG cc_start: 0.8704 (mmt-90) cc_final: 0.8422 (mmt180) REVERT: V 154 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8206 (mttt) REVERT: W 19 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8031 (mtt90) REVERT: W 46 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8269 (ttmm) REVERT: W 76 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8429 (mmt-90) REVERT: W 106 SER cc_start: 0.8637 (p) cc_final: 0.8403 (m) REVERT: W 116 LYS cc_start: 0.7715 (tttp) cc_final: 0.7477 (mtpp) REVERT: X 76 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8512 (mmt180) REVERT: X 106 SER cc_start: 0.8421 (p) cc_final: 0.8212 (m) REVERT: X 138 GLN cc_start: 0.9141 (tp40) cc_final: 0.8911 (tp-100) outliers start: 241 outliers final: 61 residues processed: 1234 average time/residue: 0.7685 time to fit residues: 1112.8972 Evaluate side-chains 1100 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1030 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 58 GLU Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 89 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 86 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain U residue 86 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain V residue 154 LYS Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 260 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 397 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN C 72 GLN C 95 ASN C 102 HIS D 80 GLN D 95 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 95 ASN F 95 ASN F 102 HIS G 95 ASN H 20 GLN H 108 ASN K 10 HIS K 57 HIS K 72 GLN L 8 ASN L 95 ASN M 57 HIS M 108 ASN N 8 ASN N 102 HIS O 8 ASN P 72 GLN Q 72 GLN R 10 HIS R 115 HIS S 95 ASN T 95 ASN U 95 ASN U 108 ASN V 72 GLN V 95 ASN W 72 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.110030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.086969 restraints weight = 289671.712| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.80 r_work: 0.2549 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36312 Z= 0.142 Angle : 0.548 6.624 49104 Z= 0.304 Chirality : 0.039 0.143 5112 Planarity : 0.004 0.052 6480 Dihedral : 13.026 178.799 4976 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.46 % Allowed : 0.97 % Favored : 98.57 % Rotamer: Outliers : 2.16 % Allowed : 24.28 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.12), residues: 4320 helix: 2.86 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -1.06 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.021 0.002 TYR P 134 PHE 0.014 0.002 PHE R 38 TRP 0.012 0.001 TRP I 90 HIS 0.007 0.001 HIS N 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (36312) covalent geometry : angle 0.54831 / 0.30 (49104) hydrogen bonds : bond 0.06080 / 4.05 ( 2640) hydrogen bonds : angle 3.77163 / 2.74 ( 7776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1133 time to evaluate : 1.423 Fit side-chains REVERT: A 41 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7396 (p0) REVERT: A 42 ASP cc_start: 0.8565 (p0) cc_final: 0.8300 (p0) REVERT: A 46 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7893 (ttmm) REVERT: A 62 HIS cc_start: 0.8381 (m170) cc_final: 0.8163 (m170) REVERT: A 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7496 (ttpp) REVERT: A 76 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.8336 (mpt180) REVERT: A 141 SER cc_start: 0.8771 (m) cc_final: 0.8442 (p) REVERT: B 41 ASP cc_start: 0.8424 (p0) cc_final: 0.7338 (p0) REVERT: B 42 ASP cc_start: 0.8387 (p0) cc_final: 0.8131 (p0) REVERT: B 46 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7921 (ttmm) REVERT: B 62 HIS cc_start: 0.8373 (m170) cc_final: 0.8154 (m170) REVERT: B 68 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7446 (ttpp) REVERT: B 141 SER cc_start: 0.8731 (m) cc_final: 0.8518 (p) REVERT: C 41 ASP cc_start: 0.8376 (p0) cc_final: 0.7403 (p0) REVERT: C 46 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7898 (ttmm) REVERT: C 68 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7342 (ttpp) REVERT: C 76 ARG cc_start: 0.8693 (mmt-90) cc_final: 0.8141 (mmt180) REVERT: C 78 PHE cc_start: 0.8964 (m-80) cc_final: 0.8529 (m-80) REVERT: C 141 SER cc_start: 0.8751 (m) cc_final: 0.8469 (m) REVERT: D 41 ASP cc_start: 0.8328 (p0) cc_final: 0.7225 (p0) REVERT: D 42 ASP cc_start: 0.8518 (p0) cc_final: 0.8248 (p0) REVERT: D 46 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7741 (ttmm) REVERT: D 62 HIS cc_start: 0.8396 (m170) cc_final: 0.8186 (m170) REVERT: D 68 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7435 (ttpp) REVERT: D 76 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.8332 (mpt180) REVERT: D 78 PHE cc_start: 0.8923 (m-80) cc_final: 0.8553 (m-80) REVERT: D 141 SER cc_start: 0.8715 (m) cc_final: 0.8385 (p) REVERT: E 41 ASP cc_start: 0.8440 (p0) cc_final: 0.7416 (p0) REVERT: E 46 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7930 (ttmm) REVERT: E 68 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7360 (ttpp) REVERT: E 76 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8401 (mmt180) REVERT: F 41 ASP cc_start: 0.8471 (p0) cc_final: 0.7315 (p0) REVERT: F 46 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7781 (ttmm) REVERT: F 68 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7359 (ttpp) REVERT: G 41 ASP cc_start: 0.8335 (p0) cc_final: 0.7367 (p0) REVERT: G 42 ASP cc_start: 0.8532 (p0) cc_final: 0.8234 (p0) REVERT: G 46 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7919 (ttmm) REVERT: G 68 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7396 (ttpp) REVERT: G 76 ARG cc_start: 0.8837 (mmt-90) cc_final: 0.8516 (mmt180) REVERT: G 106 SER cc_start: 0.8447 (p) cc_final: 0.8213 (m) REVERT: G 141 SER cc_start: 0.8760 (m) cc_final: 0.8480 (m) REVERT: H 41 ASP cc_start: 0.8538 (p0) cc_final: 0.7588 (p0) REVERT: H 42 ASP cc_start: 0.8588 (p0) cc_final: 0.8351 (p0) REVERT: H 68 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7435 (ttpp) REVERT: H 76 ARG cc_start: 0.8697 (mmt-90) cc_final: 0.8384 (mpt180) REVERT: H 141 SER cc_start: 0.8759 (m) cc_final: 0.8545 (p) REVERT: I 46 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7816 (ttmm) REVERT: I 68 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7444 (ttpp) REVERT: I 76 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8289 (mmt180) REVERT: I 141 SER cc_start: 0.8765 (m) cc_final: 0.8558 (m) REVERT: J 8 ASN cc_start: 0.8887 (t0) cc_final: 0.8509 (t0) REVERT: J 41 ASP cc_start: 0.8283 (p0) cc_final: 0.7321 (p0) REVERT: J 42 ASP cc_start: 0.8726 (p0) cc_final: 0.8358 (p0) REVERT: J 46 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7805 (ttmm) REVERT: J 68 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7468 (ttpp) REVERT: K 42 ASP cc_start: 0.8587 (p0) cc_final: 0.8344 (p0) REVERT: K 46 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7883 (ttmm) REVERT: K 68 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7453 (ttpp) REVERT: K 76 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8287 (mpt180) REVERT: K 81 ASP cc_start: 0.8409 (m-30) cc_final: 0.8059 (m-30) REVERT: K 106 SER cc_start: 0.8413 (p) cc_final: 0.8181 (m) REVERT: K 141 SER cc_start: 0.8712 (m) cc_final: 0.8428 (m) REVERT: L 41 ASP cc_start: 0.7967 (p0) cc_final: 0.7064 (p0) REVERT: L 42 ASP cc_start: 0.8459 (p0) cc_final: 0.8115 (p0) REVERT: L 46 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7899 (ttmm) REVERT: L 68 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7415 (ttpp) REVERT: L 76 ARG cc_start: 0.8652 (mmt-90) cc_final: 0.8206 (mpt180) REVERT: L 141 SER cc_start: 0.8705 (m) cc_final: 0.8447 (m) REVERT: M 46 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7829 (ttmm) REVERT: M 61 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7452 (pt0) REVERT: M 68 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7439 (ttpp) REVERT: M 76 ARG cc_start: 0.8788 (mmt-90) cc_final: 0.8543 (mpt180) REVERT: M 141 SER cc_start: 0.8730 (m) cc_final: 0.8472 (p) REVERT: N 46 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7864 (ttmm) REVERT: N 62 HIS cc_start: 0.8370 (m170) cc_final: 0.8094 (m170) REVERT: N 68 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7433 (ttpp) REVERT: N 76 ARG cc_start: 0.8740 (mmt-90) cc_final: 0.8377 (mmt180) REVERT: N 141 SER cc_start: 0.8729 (m) cc_final: 0.8433 (p) REVERT: O 46 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7938 (ttmm) REVERT: O 62 HIS cc_start: 0.8440 (m170) cc_final: 0.8206 (m170) REVERT: O 68 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7573 (ttpp) REVERT: O 76 ARG cc_start: 0.8715 (mmt-90) cc_final: 0.8262 (mpt180) REVERT: O 141 SER cc_start: 0.8725 (m) cc_final: 0.8507 (m) REVERT: P 41 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7232 (p0) REVERT: P 46 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7903 (ttmm) REVERT: P 61 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7259 (pt0) REVERT: P 68 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7529 (ttpp) REVERT: P 76 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8257 (mpt180) REVERT: P 141 SER cc_start: 0.8707 (m) cc_final: 0.8476 (m) REVERT: Q 41 ASP cc_start: 0.8346 (p0) cc_final: 0.7260 (p0) REVERT: Q 42 ASP cc_start: 0.8601 (p0) cc_final: 0.8309 (p0) REVERT: Q 46 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7871 (ttmm) REVERT: Q 68 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7465 (ttpp) REVERT: Q 141 SER cc_start: 0.8695 (m) cc_final: 0.8495 (p) REVERT: R 41 ASP cc_start: 0.7961 (p0) cc_final: 0.7057 (p0) REVERT: R 46 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7981 (ttmm) REVERT: R 62 HIS cc_start: 0.8400 (m170) cc_final: 0.8191 (m170) REVERT: R 68 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7384 (ttpp) REVERT: R 76 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8510 (mmt180) REVERT: R 81 ASP cc_start: 0.8471 (m-30) cc_final: 0.8077 (m-30) REVERT: R 141 SER cc_start: 0.8783 (m) cc_final: 0.8516 (m) REVERT: S 41 ASP cc_start: 0.8477 (p0) cc_final: 0.7347 (p0) REVERT: S 42 ASP cc_start: 0.8596 (p0) cc_final: 0.8327 (p0) REVERT: S 46 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7937 (ttmm) REVERT: S 61 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7301 (pt0) REVERT: S 68 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7472 (ttpp) REVERT: S 76 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8187 (mmt180) REVERT: T 41 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.6964 (p0) REVERT: T 42 ASP cc_start: 0.8456 (p0) cc_final: 0.8165 (p0) REVERT: T 46 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7780 (ttmm) REVERT: T 68 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7428 (ttpp) REVERT: T 76 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8421 (mmt180) REVERT: T 141 SER cc_start: 0.8744 (m) cc_final: 0.8488 (m) REVERT: U 41 ASP cc_start: 0.8287 (p0) cc_final: 0.7159 (p0) REVERT: U 42 ASP cc_start: 0.8457 (p0) cc_final: 0.8229 (p0) REVERT: U 68 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7353 (ttpp) REVERT: U 76 ARG cc_start: 0.8791 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: U 141 SER cc_start: 0.8717 (m) cc_final: 0.8469 (p) REVERT: V 41 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7518 (p0) REVERT: V 46 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7847 (ttmm) REVERT: V 68 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7549 (ttpp) REVERT: V 76 ARG cc_start: 0.8661 (mmt-90) cc_final: 0.8448 (mpt180) REVERT: V 141 SER cc_start: 0.8773 (m) cc_final: 0.8540 (m) REVERT: W 8 ASN cc_start: 0.8823 (t0) cc_final: 0.8473 (t0) REVERT: W 41 ASP cc_start: 0.8318 (p0) cc_final: 0.7224 (p0) REVERT: W 42 ASP cc_start: 0.8474 (p0) cc_final: 0.8179 (p0) REVERT: W 46 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7834 (ttmm) REVERT: W 68 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7462 (ttpp) REVERT: W 141 SER cc_start: 0.8757 (m) cc_final: 0.8473 (m) REVERT: X 41 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7312 (p0) REVERT: X 42 ASP cc_start: 0.8584 (p0) cc_final: 0.8333 (p0) REVERT: X 46 LYS cc_start: 0.8292 (ttpp) cc_final: 0.7888 (ttmm) REVERT: X 62 HIS cc_start: 0.8391 (m170) cc_final: 0.8173 (m170) REVERT: X 68 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7482 (ttpp) REVERT: X 76 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8449 (mpt180) REVERT: X 141 SER cc_start: 0.8757 (m) cc_final: 0.8485 (m) outliers start: 55 outliers final: 9 residues processed: 1146 average time/residue: 0.7286 time to fit residues: 986.6591 Evaluate side-chains 999 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 985 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain X residue 41 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 33 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 95 ASN B 95 ASN C 102 HIS D 8 ASN F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 95 ASN I 8 ASN K 8 ASN L 8 ASN M 8 ASN O 8 ASN O 95 ASN P 8 ASN P 95 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN X 8 ASN X 95 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.080862 restraints weight = 297432.737| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.74 r_work: 0.2528 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36312 Z= 0.208 Angle : 0.583 7.161 49104 Z= 0.317 Chirality : 0.041 0.145 5112 Planarity : 0.004 0.034 6480 Dihedral : 13.062 179.986 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.67 % Favored : 97.92 % Rotamer: Outliers : 3.01 % Allowed : 25.46 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.14 (0.12), residues: 4320 helix: 3.58 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.88 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 76 TYR 0.018 0.002 TYR P 134 PHE 0.019 0.002 PHE B 38 TRP 0.008 0.001 TRP Q 90 HIS 0.007 0.001 HIS F 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (36312) covalent geometry : angle 0.58327 / 0.32 (49104) hydrogen bonds : bond 0.08150 / 5.42 ( 2640) hydrogen bonds : angle 3.67983 / 2.67 ( 7776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 985 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.7605 (p0) REVERT: A 42 ASP cc_start: 0.8809 (p0) cc_final: 0.8481 (p0) REVERT: A 68 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7784 (ttpp) REVERT: A 76 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.8497 (mmt180) REVERT: B 42 ASP cc_start: 0.8766 (p0) cc_final: 0.8527 (p0) REVERT: B 46 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8282 (ttmm) REVERT: B 68 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7791 (ttpp) REVERT: C 41 ASP cc_start: 0.8632 (p0) cc_final: 0.7746 (p0) REVERT: C 42 ASP cc_start: 0.8678 (p0) cc_final: 0.8449 (p0) REVERT: C 46 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8224 (ttmm) REVERT: C 68 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7747 (ttpp) REVERT: C 76 ARG cc_start: 0.8912 (mmt-90) cc_final: 0.8570 (mmt180) REVERT: D 41 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.7620 (p0) REVERT: D 42 ASP cc_start: 0.8753 (p0) cc_final: 0.8455 (p0) REVERT: D 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8181 (ttmm) REVERT: D 68 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7747 (ttpp) REVERT: D 76 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8448 (mmt180) REVERT: D 110 SER cc_start: 0.9077 (t) cc_final: 0.8798 (m) REVERT: E 41 ASP cc_start: 0.8729 (p0) cc_final: 0.7679 (p0) REVERT: E 68 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7745 (ttpp) REVERT: E 76 ARG cc_start: 0.8961 (mmt-90) cc_final: 0.8634 (mpt180) REVERT: E 110 SER cc_start: 0.8948 (t) cc_final: 0.8740 (p) REVERT: F 41 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.7738 (p0) REVERT: F 61 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7526 (pt0) REVERT: F 68 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7733 (ttpp) REVERT: G 42 ASP cc_start: 0.8772 (p0) cc_final: 0.8465 (p0) REVERT: G 68 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7766 (ttpp) REVERT: G 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8545 (mmt180) REVERT: H 42 ASP cc_start: 0.8800 (p0) cc_final: 0.8499 (p0) REVERT: H 68 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7777 (ttpp) REVERT: H 76 ARG cc_start: 0.8898 (mmt-90) cc_final: 0.8210 (mmt180) REVERT: H 141 SER cc_start: 0.8904 (m) cc_final: 0.8665 (m) REVERT: I 41 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.7675 (p0) REVERT: I 68 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7715 (ttpp) REVERT: I 76 ARG cc_start: 0.8925 (mmt-90) cc_final: 0.8551 (mpt180) REVERT: I 141 SER cc_start: 0.8901 (m) cc_final: 0.8661 (m) REVERT: J 41 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7561 (p0) REVERT: J 42 ASP cc_start: 0.8786 (p0) cc_final: 0.8366 (p0) REVERT: J 46 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8100 (ttmm) REVERT: J 68 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7747 (ttpp) REVERT: K 42 ASP cc_start: 0.8771 (p0) cc_final: 0.8490 (p0) REVERT: K 46 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8221 (ttmm) REVERT: K 68 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7802 (ttpp) REVERT: K 76 ARG cc_start: 0.8840 (mmt-90) cc_final: 0.8186 (mpt180) REVERT: K 81 ASP cc_start: 0.8605 (m-30) cc_final: 0.8360 (m-30) REVERT: L 41 ASP cc_start: 0.8529 (p0) cc_final: 0.7693 (p0) REVERT: L 68 LYS cc_start: 0.8467 (mtpp) cc_final: 0.7854 (ttpp) REVERT: L 76 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8497 (mpt180) REVERT: M 8 ASN cc_start: 0.9083 (t0) cc_final: 0.8874 (t0) REVERT: M 41 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.7786 (p0) REVERT: M 42 ASP cc_start: 0.8864 (p0) cc_final: 0.8626 (p0) REVERT: M 46 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8121 (ttmm) REVERT: M 68 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7753 (ttpp) REVERT: M 76 ARG cc_start: 0.8986 (mmt-90) cc_final: 0.8567 (mmt180) REVERT: M 141 SER cc_start: 0.8861 (m) cc_final: 0.8615 (m) REVERT: N 42 ASP cc_start: 0.8910 (p0) cc_final: 0.8698 (p0) REVERT: N 68 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7802 (ttpp) REVERT: N 76 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8470 (mpt180) REVERT: O 46 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8179 (ttmm) REVERT: O 68 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7823 (ttpp) REVERT: O 76 ARG cc_start: 0.8848 (mmt-90) cc_final: 0.8329 (mpt180) REVERT: O 141 SER cc_start: 0.8861 (m) cc_final: 0.8626 (m) REVERT: P 41 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.7666 (p0) REVERT: P 68 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7844 (ttpp) REVERT: P 76 ARG cc_start: 0.8903 (mmt-90) cc_final: 0.8326 (mmt180) REVERT: P 141 SER cc_start: 0.8846 (m) cc_final: 0.8614 (m) REVERT: Q 41 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.7660 (p0) REVERT: Q 42 ASP cc_start: 0.8785 (p0) cc_final: 0.8474 (p0) REVERT: Q 46 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8216 (ttmm) REVERT: Q 68 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7739 (ttpp) REVERT: Q 76 ARG cc_start: 0.8810 (mpt180) cc_final: 0.8519 (mmt180) REVERT: R 41 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7525 (p0) REVERT: R 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8297 (ttmm) REVERT: R 68 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7726 (ttpp) REVERT: R 76 ARG cc_start: 0.8925 (mmt-90) cc_final: 0.8410 (mmt180) REVERT: R 81 ASP cc_start: 0.8583 (m-30) cc_final: 0.8311 (m-30) REVERT: S 41 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.7669 (p0) REVERT: S 42 ASP cc_start: 0.8781 (p0) cc_final: 0.8449 (p0) REVERT: S 46 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8219 (ttmm) REVERT: S 68 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7758 (ttpp) REVERT: S 76 ARG cc_start: 0.8788 (mmt-90) cc_final: 0.8450 (mmt-90) REVERT: T 41 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7706 (p0) REVERT: T 42 ASP cc_start: 0.8699 (p0) cc_final: 0.8362 (p0) REVERT: T 46 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8129 (ttmm) REVERT: T 68 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7744 (ttpp) REVERT: T 76 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8464 (mmt180) REVERT: U 41 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.7682 (p0) REVERT: U 42 ASP cc_start: 0.8757 (p0) cc_final: 0.8483 (p0) REVERT: U 46 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8188 (ttmm) REVERT: U 68 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7712 (ttpp) REVERT: U 76 ARG cc_start: 0.8954 (mmt-90) cc_final: 0.8610 (mmt180) REVERT: U 110 SER cc_start: 0.8945 (t) cc_final: 0.8740 (p) REVERT: U 141 SER cc_start: 0.8859 (m) cc_final: 0.8626 (m) REVERT: V 41 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.7763 (p0) REVERT: V 68 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7777 (ttpp) REVERT: V 76 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8579 (mpt180) REVERT: V 141 SER cc_start: 0.8907 (m) cc_final: 0.8629 (m) REVERT: W 41 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.7556 (p0) REVERT: W 42 ASP cc_start: 0.8718 (p0) cc_final: 0.8363 (p0) REVERT: W 68 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7764 (ttpp) REVERT: W 76 ARG cc_start: 0.8761 (mpt180) cc_final: 0.8485 (mmt180) REVERT: X 42 ASP cc_start: 0.8808 (p0) cc_final: 0.8567 (p0) REVERT: X 68 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7776 (ttpp) REVERT: X 76 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8483 (mpt180) outliers start: 87 outliers final: 38 residues processed: 1022 average time/residue: 0.7115 time to fit residues: 866.3413 Evaluate side-chains 1007 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 955 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 chunk 363 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN C 102 HIS D 8 ASN E 138 GLN F 8 ASN F 102 HIS G 8 ASN I 8 ASN J 95 ASN K 8 ASN L 8 ASN M 95 ASN M 138 GLN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN Q 95 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.110438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.087224 restraints weight = 296395.497| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.80 r_work: 0.2547 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 36312 Z= 0.132 Angle : 0.490 5.942 49104 Z= 0.270 Chirality : 0.037 0.128 5112 Planarity : 0.003 0.032 6480 Dihedral : 12.960 179.421 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.28 % Favored : 98.33 % Rotamer: Outliers : 2.78 % Allowed : 26.18 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.89 (0.12), residues: 4320 helix: 4.04 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.44 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 76 TYR 0.017 0.001 TYR I 37 PHE 0.014 0.002 PHE F 38 TRP 0.008 0.001 TRP N 90 HIS 0.006 0.001 HIS F 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (36312) covalent geometry : angle 0.48993 / 0.27 (49104) hydrogen bonds : bond 0.05666 / 3.77 ( 2640) hydrogen bonds : angle 3.40671 / 2.47 ( 7776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1000 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7389 (p0) REVERT: A 42 ASP cc_start: 0.8507 (p0) cc_final: 0.8243 (p0) REVERT: A 46 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7952 (ttmm) REVERT: A 68 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7605 (ttpp) REVERT: A 76 ARG cc_start: 0.8768 (mmt-90) cc_final: 0.8431 (mmt180) REVERT: A 141 SER cc_start: 0.8745 (m) cc_final: 0.8467 (m) REVERT: B 41 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7333 (p0) REVERT: B 46 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7957 (ttmm) REVERT: B 68 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7620 (ttpp) REVERT: C 41 ASP cc_start: 0.8405 (p0) cc_final: 0.7470 (p0) REVERT: C 46 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7930 (ttmm) REVERT: C 68 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7565 (ttpp) REVERT: C 76 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.8558 (mmt180) REVERT: C 141 SER cc_start: 0.8731 (m) cc_final: 0.8443 (m) REVERT: D 41 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7216 (p0) REVERT: D 42 ASP cc_start: 0.8353 (p0) cc_final: 0.8123 (p0) REVERT: D 46 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7923 (ttmm) REVERT: D 68 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7593 (ttpp) REVERT: D 76 ARG cc_start: 0.8750 (mmt-90) cc_final: 0.8344 (mmt180) REVERT: D 141 SER cc_start: 0.8724 (m) cc_final: 0.8461 (m) REVERT: E 41 ASP cc_start: 0.8421 (p0) cc_final: 0.7275 (p0) REVERT: E 46 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7957 (ttmm) REVERT: E 68 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7523 (ttpp) REVERT: E 76 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.8488 (mpt180) REVERT: E 110 SER cc_start: 0.8873 (t) cc_final: 0.8641 (p) REVERT: F 41 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7282 (p0) REVERT: F 46 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7905 (ttmm) REVERT: F 61 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7419 (pt0) REVERT: F 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7553 (ttpp) REVERT: G 41 ASP cc_start: 0.8494 (p0) cc_final: 0.7529 (p0) REVERT: G 42 ASP cc_start: 0.8460 (p0) cc_final: 0.8204 (p0) REVERT: G 46 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7995 (ttmm) REVERT: G 68 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7583 (ttpp) REVERT: G 76 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8493 (mmt180) REVERT: G 141 SER cc_start: 0.8747 (m) cc_final: 0.8487 (m) REVERT: H 41 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7532 (p0) REVERT: H 42 ASP cc_start: 0.8461 (p0) cc_final: 0.8245 (p0) REVERT: H 68 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7616 (ttpp) REVERT: H 76 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8204 (mmt180) REVERT: H 141 SER cc_start: 0.8823 (m) cc_final: 0.8609 (m) REVERT: I 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7359 (p0) REVERT: I 46 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7939 (ttmm) REVERT: I 68 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7513 (ttpp) REVERT: I 76 ARG cc_start: 0.8761 (mmt-90) cc_final: 0.8332 (mpt180) REVERT: I 141 SER cc_start: 0.8803 (m) cc_final: 0.8586 (m) REVERT: J 41 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7306 (p0) REVERT: J 46 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7799 (mttp) REVERT: J 61 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7492 (pt0) REVERT: J 68 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7509 (ttpp) REVERT: K 41 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7387 (p0) REVERT: K 46 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7907 (ttmm) REVERT: K 68 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7643 (ttpp) REVERT: K 76 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8175 (mpt180) REVERT: K 81 ASP cc_start: 0.8592 (m-30) cc_final: 0.8251 (m-30) REVERT: K 141 SER cc_start: 0.8703 (m) cc_final: 0.8433 (m) REVERT: L 41 ASP cc_start: 0.8224 (p0) cc_final: 0.7350 (p0) REVERT: L 46 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7962 (ttmm) REVERT: L 68 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7660 (ttpp) REVERT: L 76 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8413 (mpt180) REVERT: L 141 SER cc_start: 0.8733 (m) cc_final: 0.8465 (m) REVERT: M 41 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7362 (p0) REVERT: M 42 ASP cc_start: 0.8515 (p0) cc_final: 0.8312 (p0) REVERT: M 46 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7782 (mttp) REVERT: M 68 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7626 (ttpp) REVERT: M 76 ARG cc_start: 0.8895 (mmt-90) cc_final: 0.8580 (mpt180) REVERT: M 141 SER cc_start: 0.8799 (m) cc_final: 0.8582 (m) REVERT: N 41 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.7631 (p0) REVERT: N 46 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7943 (ttmm) REVERT: N 68 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7618 (ttpp) REVERT: N 76 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8197 (mmt180) REVERT: N 141 SER cc_start: 0.8743 (m) cc_final: 0.8475 (m) REVERT: O 41 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7557 (p0) REVERT: O 42 ASP cc_start: 0.8727 (p0) cc_final: 0.8438 (p0) REVERT: O 46 LYS cc_start: 0.8385 (ttpp) cc_final: 0.7858 (ttmm) REVERT: O 68 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7560 (ttpp) REVERT: O 76 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8262 (mpt180) REVERT: O 141 SER cc_start: 0.8759 (m) cc_final: 0.8543 (m) REVERT: P 41 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7306 (p0) REVERT: P 46 LYS cc_start: 0.8396 (ttpp) cc_final: 0.7978 (ttmm) REVERT: P 68 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7637 (ttpp) REVERT: P 76 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8281 (mpt180) REVERT: P 141 SER cc_start: 0.8766 (m) cc_final: 0.8527 (m) REVERT: Q 41 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7253 (p0) REVERT: Q 46 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7945 (ttmm) REVERT: Q 68 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7531 (ttpp) REVERT: R 41 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7137 (p0) REVERT: R 68 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7510 (ttpp) REVERT: R 76 ARG cc_start: 0.8804 (mmt-90) cc_final: 0.8330 (mmt180) REVERT: R 81 ASP cc_start: 0.8587 (m-30) cc_final: 0.8224 (m-30) REVERT: R 106 SER cc_start: 0.8521 (p) cc_final: 0.8248 (m) REVERT: R 141 SER cc_start: 0.8752 (m) cc_final: 0.8489 (m) REVERT: S 41 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7345 (p0) REVERT: S 46 LYS cc_start: 0.8325 (ttpp) cc_final: 0.7981 (ttmm) REVERT: S 68 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7563 (ttpp) REVERT: S 76 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8301 (mpt180) REVERT: S 83 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8386 (mmtt) REVERT: T 41 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7236 (p0) REVERT: T 46 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7791 (mttp) REVERT: T 68 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7529 (ttpp) REVERT: T 76 ARG cc_start: 0.8787 (mmt-90) cc_final: 0.8384 (mmt180) REVERT: T 141 SER cc_start: 0.8711 (m) cc_final: 0.8434 (m) REVERT: U 41 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7237 (p0) REVERT: U 42 ASP cc_start: 0.8386 (p0) cc_final: 0.8146 (p0) REVERT: U 46 LYS cc_start: 0.8394 (ttpp) cc_final: 0.7887 (ttmm) REVERT: U 68 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7525 (ttpp) REVERT: U 76 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8527 (mmt180) REVERT: U 110 SER cc_start: 0.8880 (t) cc_final: 0.8651 (p) REVERT: U 141 SER cc_start: 0.8773 (m) cc_final: 0.8567 (m) REVERT: V 41 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7285 (p0) REVERT: V 46 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7934 (ttmm) REVERT: V 68 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7566 (ttpp) REVERT: V 76 ARG cc_start: 0.8781 (mmt-90) cc_final: 0.8474 (mpt180) REVERT: V 141 SER cc_start: 0.8790 (m) cc_final: 0.8547 (m) REVERT: W 41 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7188 (p0) REVERT: W 46 LYS cc_start: 0.8297 (ttpp) cc_final: 0.7922 (ttmm) REVERT: W 68 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7594 (ttpp) REVERT: W 141 SER cc_start: 0.8721 (m) cc_final: 0.8428 (m) REVERT: X 41 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7326 (p0) REVERT: X 42 ASP cc_start: 0.8438 (p0) cc_final: 0.8178 (p0) REVERT: X 46 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7963 (ttmm) REVERT: X 68 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7569 (ttpp) REVERT: X 76 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8519 (mpt180) REVERT: X 141 SER cc_start: 0.8719 (m) cc_final: 0.8442 (m) outliers start: 79 outliers final: 34 residues processed: 1033 average time/residue: 0.7209 time to fit residues: 886.3552 Evaluate side-chains 1007 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 952 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 251 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN Q 102 HIS R 8 ASN R 138 GLN S 8 ASN S 102 HIS S 138 GLN T 8 ASN T 102 HIS T 138 GLN U 8 ASN V 8 ASN V 102 HIS W 20 GLN W 138 GLN X 8 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.088480 restraints weight = 308701.649| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.90 r_work: 0.2631 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 36312 Z= 0.121 Angle : 0.470 5.705 49104 Z= 0.258 Chirality : 0.036 0.126 5112 Planarity : 0.003 0.033 6480 Dihedral : 12.947 179.722 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.33 % Favored : 98.28 % Rotamer: Outliers : 2.47 % Allowed : 26.26 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.28 (0.12), residues: 4320 helix: 4.30 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.26 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 76 TYR 0.016 0.001 TYR I 37 PHE 0.012 0.002 PHE F 38 TRP 0.006 0.001 TRP N 90 HIS 0.006 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (36312) covalent geometry : angle 0.46963 / 0.26 (49104) hydrogen bonds : bond 0.05100 / 3.39 ( 2640) hydrogen bonds : angle 3.26829 / 2.38 ( 7776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 983 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7393 (p0) REVERT: A 42 ASP cc_start: 0.8382 (p0) cc_final: 0.8126 (p0) REVERT: A 46 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7827 (mttp) REVERT: A 68 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7752 (ttpp) REVERT: A 76 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: A 110 SER cc_start: 0.8977 (t) cc_final: 0.8767 (p) REVERT: A 141 SER cc_start: 0.8780 (m) cc_final: 0.8550 (m) REVERT: B 41 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7235 (p0) REVERT: B 46 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7767 (mttp) REVERT: B 62 HIS cc_start: 0.8409 (m170) cc_final: 0.8183 (m170) REVERT: B 68 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7705 (ttpp) REVERT: B 110 SER cc_start: 0.8979 (t) cc_final: 0.8766 (p) REVERT: C 41 ASP cc_start: 0.8307 (p0) cc_final: 0.7443 (p0) REVERT: C 46 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7848 (mttp) REVERT: C 110 SER cc_start: 0.8997 (t) cc_final: 0.8759 (p) REVERT: C 141 SER cc_start: 0.8778 (m) cc_final: 0.8558 (m) REVERT: D 41 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7205 (p0) REVERT: D 46 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7816 (mttp) REVERT: D 68 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7712 (ttpp) REVERT: D 76 ARG cc_start: 0.8801 (mmt-90) cc_final: 0.8400 (mmt180) REVERT: D 141 SER cc_start: 0.8796 (m) cc_final: 0.8558 (m) REVERT: E 41 ASP cc_start: 0.8243 (p0) cc_final: 0.7125 (p0) REVERT: E 46 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7952 (ttmm) REVERT: E 68 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7547 (ttpp) REVERT: E 76 ARG cc_start: 0.8883 (mmt-90) cc_final: 0.8521 (mpt180) REVERT: E 110 SER cc_start: 0.8939 (t) cc_final: 0.8703 (p) REVERT: F 41 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7061 (p0) REVERT: F 61 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7532 (pt0) REVERT: F 68 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7635 (ttpp) REVERT: G 41 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7486 (p0) REVERT: G 42 ASP cc_start: 0.8333 (p0) cc_final: 0.8127 (p0) REVERT: G 46 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7977 (ttmm) REVERT: G 68 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7707 (ttpp) REVERT: G 76 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: H 41 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7498 (p0) REVERT: H 68 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7747 (ttpp) REVERT: H 76 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8503 (mpt180) REVERT: H 110 SER cc_start: 0.8997 (t) cc_final: 0.8793 (p) REVERT: I 41 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7174 (p0) REVERT: I 46 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7925 (ttmm) REVERT: I 68 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7599 (ttpp) REVERT: I 76 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8420 (mpt180) REVERT: I 110 SER cc_start: 0.8948 (t) cc_final: 0.8746 (p) REVERT: J 41 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7224 (p0) REVERT: J 46 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7853 (mttp) REVERT: J 61 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7592 (pt0) REVERT: J 68 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7568 (ttpp) REVERT: J 110 SER cc_start: 0.8932 (t) cc_final: 0.8713 (p) REVERT: K 41 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7175 (p0) REVERT: K 46 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7793 (mttp) REVERT: K 68 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7745 (ttpp) REVERT: K 76 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8252 (mpt180) REVERT: K 81 ASP cc_start: 0.8630 (m-30) cc_final: 0.8313 (m-30) REVERT: K 110 SER cc_start: 0.8976 (t) cc_final: 0.8759 (p) REVERT: K 141 SER cc_start: 0.8769 (m) cc_final: 0.8509 (m) REVERT: L 41 ASP cc_start: 0.8201 (p0) cc_final: 0.7350 (p0) REVERT: L 46 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7968 (ttmm) REVERT: L 68 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7692 (ttpp) REVERT: L 76 ARG cc_start: 0.8717 (mmt-90) cc_final: 0.8370 (mpt180) REVERT: L 141 SER cc_start: 0.8771 (m) cc_final: 0.8554 (m) REVERT: M 41 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7307 (p0) REVERT: M 46 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7900 (mttp) REVERT: M 68 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7544 (ttpp) REVERT: M 76 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8242 (mmt180) REVERT: M 78 PHE cc_start: 0.8942 (m-80) cc_final: 0.8686 (m-80) REVERT: M 110 SER cc_start: 0.8953 (t) cc_final: 0.8743 (p) REVERT: M 141 SER cc_start: 0.8841 (m) cc_final: 0.8640 (m) REVERT: N 41 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7467 (p0) REVERT: N 46 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7972 (ttmm) REVERT: N 68 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7722 (ttpp) REVERT: N 76 ARG cc_start: 0.8694 (mmt-90) cc_final: 0.8273 (mmt180) REVERT: N 110 SER cc_start: 0.8940 (t) cc_final: 0.8739 (p) REVERT: N 141 SER cc_start: 0.8797 (m) cc_final: 0.8568 (m) REVERT: O 41 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7499 (p0) REVERT: O 42 ASP cc_start: 0.8584 (p0) cc_final: 0.8345 (p0) REVERT: O 46 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7869 (mttp) REVERT: O 68 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7674 (ttpp) REVERT: O 76 ARG cc_start: 0.8789 (mmt-90) cc_final: 0.8343 (mpt180) REVERT: O 110 SER cc_start: 0.8935 (t) cc_final: 0.8731 (p) REVERT: O 141 SER cc_start: 0.8843 (m) cc_final: 0.8636 (m) REVERT: P 41 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7352 (p0) REVERT: P 46 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7847 (mttp) REVERT: P 76 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8371 (mpt180) REVERT: P 110 SER cc_start: 0.8989 (t) cc_final: 0.8778 (p) REVERT: Q 41 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7040 (p0) REVERT: Q 46 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7818 (mttp) REVERT: Q 68 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7565 (ttpp) REVERT: Q 110 SER cc_start: 0.8987 (t) cc_final: 0.8784 (p) REVERT: R 41 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7212 (p0) REVERT: R 68 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7585 (ttpp) REVERT: R 76 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8419 (mmt180) REVERT: R 81 ASP cc_start: 0.8632 (m-30) cc_final: 0.8280 (m-30) REVERT: R 141 SER cc_start: 0.8817 (m) cc_final: 0.8585 (m) REVERT: S 41 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7145 (p0) REVERT: S 46 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7818 (mttp) REVERT: S 68 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7590 (ttpp) REVERT: S 76 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8375 (mpt180) REVERT: S 83 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8427 (mmtm) REVERT: T 41 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7150 (p0) REVERT: T 46 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7789 (mttp) REVERT: T 68 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7619 (ttpp) REVERT: T 76 ARG cc_start: 0.8822 (mmt-90) cc_final: 0.8488 (mmt180) REVERT: T 141 SER cc_start: 0.8799 (m) cc_final: 0.8577 (m) REVERT: U 41 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7125 (p0) REVERT: U 46 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7860 (mttp) REVERT: U 68 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7622 (ttpp) REVERT: U 76 ARG cc_start: 0.8871 (mmt-90) cc_final: 0.8567 (mmt180) REVERT: U 110 SER cc_start: 0.8943 (t) cc_final: 0.8710 (p) REVERT: V 41 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7176 (p0) REVERT: V 46 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7773 (mttp) REVERT: V 68 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7748 (ttpp) REVERT: V 76 ARG cc_start: 0.8832 (mmt-90) cc_final: 0.8540 (mpt180) REVERT: V 110 SER cc_start: 0.8968 (t) cc_final: 0.8738 (p) REVERT: V 141 SER cc_start: 0.8822 (m) cc_final: 0.8610 (m) REVERT: W 41 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7052 (p0) REVERT: W 46 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7772 (mttp) REVERT: W 68 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7623 (ttpp) REVERT: W 110 SER cc_start: 0.8995 (t) cc_final: 0.8788 (p) REVERT: W 141 SER cc_start: 0.8800 (m) cc_final: 0.8583 (m) REVERT: X 41 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7284 (p0) REVERT: X 46 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7812 (mttp) REVERT: X 68 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7672 (ttpp) REVERT: X 76 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8620 (mpt180) REVERT: X 141 SER cc_start: 0.8821 (m) cc_final: 0.8591 (m) outliers start: 67 outliers final: 24 residues processed: 994 average time/residue: 0.7288 time to fit residues: 861.5570 Evaluate side-chains 1005 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 959 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS I 8 ASN I 95 ASN J 138 GLN K 8 ASN L 8 ASN L 102 HIS M 8 ASN N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN R 8 ASN S 8 ASN S 102 HIS T 8 ASN U 8 ASN V 8 ASN V 62 HIS V 102 HIS X 8 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.088040 restraints weight = 311546.937| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.91 r_work: 0.2561 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36312 Z= 0.131 Angle : 0.478 5.593 49104 Z= 0.262 Chirality : 0.037 0.129 5112 Planarity : 0.003 0.034 6480 Dihedral : 12.968 179.963 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.53 % Favored : 98.09 % Rotamer: Outliers : 2.49 % Allowed : 25.90 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.31 (0.12), residues: 4320 helix: 4.32 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.18 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 76 TYR 0.016 0.001 TYR P 134 PHE 0.013 0.002 PHE R 38 TRP 0.005 0.001 TRP Q 90 HIS 0.006 0.001 HIS F 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (36312) covalent geometry : angle 0.47847 / 0.26 (49104) hydrogen bonds : bond 0.05557 / 3.69 ( 2640) hydrogen bonds : angle 3.28708 / 2.39 ( 7776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 983 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7354 (p0) REVERT: A 42 ASP cc_start: 0.8398 (p0) cc_final: 0.8123 (p0) REVERT: A 46 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7785 (mttp) REVERT: A 68 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7584 (ttpp) REVERT: A 76 ARG cc_start: 0.8746 (mmt-90) cc_final: 0.8396 (mmt180) REVERT: A 110 SER cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: A 141 SER cc_start: 0.8721 (m) cc_final: 0.8438 (m) REVERT: B 41 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7318 (p0) REVERT: B 46 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7761 (mttp) REVERT: B 68 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7667 (ttpp) REVERT: B 110 SER cc_start: 0.8881 (t) cc_final: 0.8652 (p) REVERT: C 41 ASP cc_start: 0.8345 (p0) cc_final: 0.7516 (p0) REVERT: C 46 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7799 (mttp) REVERT: C 110 SER cc_start: 0.8914 (t) cc_final: 0.8662 (p) REVERT: C 141 SER cc_start: 0.8711 (m) cc_final: 0.8407 (m) REVERT: D 41 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7134 (p0) REVERT: D 46 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7741 (mttp) REVERT: D 68 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7622 (ttpp) REVERT: D 76 ARG cc_start: 0.8755 (mmt-90) cc_final: 0.8308 (mmt180) REVERT: D 141 SER cc_start: 0.8709 (m) cc_final: 0.8435 (m) REVERT: E 41 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7233 (p0) REVERT: E 46 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7903 (ttmm) REVERT: E 68 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7524 (ttpp) REVERT: E 76 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8500 (mpt180) REVERT: E 110 SER cc_start: 0.8866 (t) cc_final: 0.8614 (p) REVERT: F 41 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7230 (p0) REVERT: F 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7548 (ttpp) REVERT: G 41 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7525 (p0) REVERT: G 46 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7945 (ttmm) REVERT: G 68 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7647 (ttpp) REVERT: G 76 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8474 (mmt180) REVERT: H 41 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7417 (p0) REVERT: H 68 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7633 (ttpp) REVERT: H 76 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8182 (mmt180) REVERT: H 110 SER cc_start: 0.8897 (t) cc_final: 0.8676 (p) REVERT: I 41 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7234 (p0) REVERT: I 46 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7921 (ttmm) REVERT: I 68 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7552 (ttpp) REVERT: I 76 ARG cc_start: 0.8728 (mmt-90) cc_final: 0.8309 (mpt180) REVERT: I 110 SER cc_start: 0.8843 (t) cc_final: 0.8617 (p) REVERT: J 41 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7321 (p0) REVERT: J 46 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7848 (mttp) REVERT: J 68 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7551 (ttpp) REVERT: J 110 SER cc_start: 0.8853 (t) cc_final: 0.8621 (p) REVERT: K 41 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7356 (p0) REVERT: K 46 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7744 (mttp) REVERT: K 68 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7686 (ttpp) REVERT: K 76 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8124 (mpt180) REVERT: K 81 ASP cc_start: 0.8574 (m-30) cc_final: 0.8268 (m-30) REVERT: K 110 SER cc_start: 0.8900 (t) cc_final: 0.8673 (p) REVERT: K 141 SER cc_start: 0.8721 (m) cc_final: 0.8445 (m) REVERT: L 41 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7385 (p0) REVERT: L 46 LYS cc_start: 0.8331 (ttpp) cc_final: 0.7947 (ttmm) REVERT: L 68 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7650 (ttpp) REVERT: L 76 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.8351 (mpt180) REVERT: L 141 SER cc_start: 0.8715 (m) cc_final: 0.8448 (m) REVERT: M 41 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7290 (p0) REVERT: M 46 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7784 (mttp) REVERT: M 68 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7610 (ttpp) REVERT: M 76 ARG cc_start: 0.8831 (mmt-90) cc_final: 0.8139 (mmt180) REVERT: M 78 PHE cc_start: 0.8886 (m-80) cc_final: 0.8665 (m-80) REVERT: M 110 SER cc_start: 0.8860 (t) cc_final: 0.8629 (p) REVERT: M 141 SER cc_start: 0.8775 (m) cc_final: 0.8562 (m) REVERT: N 41 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7443 (p0) REVERT: N 46 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7873 (ttmm) REVERT: N 68 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7657 (ttpp) REVERT: N 76 ARG cc_start: 0.8653 (mmt-90) cc_final: 0.8324 (mpt180) REVERT: N 110 SER cc_start: 0.8842 (t) cc_final: 0.8624 (p) REVERT: N 141 SER cc_start: 0.8731 (m) cc_final: 0.8483 (m) REVERT: O 41 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7434 (p0) REVERT: O 42 ASP cc_start: 0.8525 (p0) cc_final: 0.8253 (p0) REVERT: O 46 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7840 (mttp) REVERT: O 68 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7659 (ttpp) REVERT: O 76 ARG cc_start: 0.8744 (mmt-90) cc_final: 0.8243 (mpt180) REVERT: O 110 SER cc_start: 0.8853 (t) cc_final: 0.8628 (p) REVERT: O 141 SER cc_start: 0.8756 (m) cc_final: 0.8542 (m) REVERT: P 41 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7399 (p0) REVERT: P 46 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7819 (mttp) REVERT: P 76 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8293 (mpt180) REVERT: P 110 SER cc_start: 0.8888 (t) cc_final: 0.8653 (p) REVERT: Q 41 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7157 (p0) REVERT: Q 46 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7766 (mttp) REVERT: Q 68 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7569 (ttpp) REVERT: Q 110 SER cc_start: 0.8914 (t) cc_final: 0.8703 (p) REVERT: R 41 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7250 (p0) REVERT: R 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7546 (ttpp) REVERT: R 76 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8297 (mmt180) REVERT: R 81 ASP cc_start: 0.8605 (m-30) cc_final: 0.8251 (m-30) REVERT: R 141 SER cc_start: 0.8768 (m) cc_final: 0.8509 (m) REVERT: S 41 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7254 (p0) REVERT: S 46 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7777 (mttp) REVERT: S 68 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7640 (ttpp) REVERT: S 76 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.8225 (mmt180) REVERT: S 83 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (mmtt) REVERT: T 41 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7145 (p0) REVERT: T 42 ASP cc_start: 0.8278 (p0) cc_final: 0.8069 (p0) REVERT: T 46 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7791 (mttp) REVERT: T 68 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7546 (ttpp) REVERT: T 76 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8343 (mmt180) REVERT: T 141 SER cc_start: 0.8722 (m) cc_final: 0.8453 (m) REVERT: U 41 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7132 (p0) REVERT: U 46 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7798 (mttp) REVERT: U 68 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7573 (ttpp) REVERT: U 76 ARG cc_start: 0.8818 (mmt-90) cc_final: 0.8469 (mmt180) REVERT: U 110 SER cc_start: 0.8870 (t) cc_final: 0.8623 (p) REVERT: V 41 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7247 (p0) REVERT: V 46 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7750 (mttp) REVERT: V 68 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7599 (ttpp) REVERT: V 76 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8257 (mmt180) REVERT: V 110 SER cc_start: 0.8867 (t) cc_final: 0.8615 (p) REVERT: V 141 SER cc_start: 0.8768 (m) cc_final: 0.8527 (m) REVERT: W 41 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7200 (p0) REVERT: W 46 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7763 (mttp) REVERT: W 68 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7535 (ttpp) REVERT: W 110 SER cc_start: 0.8919 (t) cc_final: 0.8691 (p) REVERT: W 141 SER cc_start: 0.8710 (m) cc_final: 0.8424 (m) REVERT: X 41 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7166 (p0) REVERT: X 46 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7768 (mttp) REVERT: X 68 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7563 (ttpp) REVERT: X 76 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8343 (mmt-90) REVERT: X 141 SER cc_start: 0.8734 (m) cc_final: 0.8462 (m) outliers start: 69 outliers final: 32 residues processed: 997 average time/residue: 0.7128 time to fit residues: 845.0693 Evaluate side-chains 1027 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 971 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 102 HIS C 62 HIS C 102 HIS D 8 ASN F 8 ASN F 102 HIS G 8 ASN I 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN U 102 HIS V 8 ASN V 62 HIS X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.082446 restraints weight = 295900.710| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.85 r_work: 0.2517 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36312 Z= 0.172 Angle : 0.528 6.076 49104 Z= 0.287 Chirality : 0.039 0.136 5112 Planarity : 0.003 0.044 6480 Dihedral : 13.015 179.999 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.60 % Favored : 98.04 % Rotamer: Outliers : 3.09 % Allowed : 25.31 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.09 (0.12), residues: 4320 helix: 4.13 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.14 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 19 TYR 0.017 0.002 TYR P 134 PHE 0.017 0.002 PHE E 38 TRP 0.005 0.001 TRP I 90 HIS 0.006 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (36312) covalent geometry : angle 0.52822 / 0.29 (49104) hydrogen bonds : bond 0.07044 / 4.68 ( 2640) hydrogen bonds : angle 3.43394 / 2.49 ( 7776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 979 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7519 (p0) REVERT: A 42 ASP cc_start: 0.8636 (p0) cc_final: 0.8284 (p0) REVERT: A 46 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8161 (ttmm) REVERT: A 68 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7805 (ttpp) REVERT: A 76 ARG cc_start: 0.8843 (mmt-90) cc_final: 0.8487 (mmt180) REVERT: A 141 SER cc_start: 0.8875 (m) cc_final: 0.8573 (m) REVERT: B 41 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.7608 (p0) REVERT: B 46 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8231 (ttmm) REVERT: B 68 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7781 (ttpp) REVERT: B 110 SER cc_start: 0.8964 (t) cc_final: 0.8732 (p) REVERT: C 41 ASP cc_start: 0.8528 (p0) cc_final: 0.7704 (p0) REVERT: C 46 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8133 (ttmm) REVERT: C 110 SER cc_start: 0.8986 (t) cc_final: 0.8745 (p) REVERT: C 141 SER cc_start: 0.8857 (m) cc_final: 0.8558 (m) REVERT: D 41 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7465 (p0) REVERT: D 46 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8029 (mttp) REVERT: D 68 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7784 (ttpp) REVERT: D 76 ARG cc_start: 0.8872 (mmt-90) cc_final: 0.8403 (mmt180) REVERT: D 141 SER cc_start: 0.8863 (m) cc_final: 0.8572 (m) REVERT: E 41 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7449 (p0) REVERT: E 46 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8140 (ttmm) REVERT: E 68 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7739 (ttpp) REVERT: E 76 ARG cc_start: 0.8960 (mmt-90) cc_final: 0.8561 (mpt180) REVERT: E 110 SER cc_start: 0.8967 (t) cc_final: 0.8718 (p) REVERT: F 41 ASP cc_start: 0.8555 (p0) cc_final: 0.7578 (p0) REVERT: F 68 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7735 (ttpp) REVERT: G 41 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7688 (p0) REVERT: G 46 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8181 (ttmm) REVERT: G 68 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7750 (ttpp) REVERT: G 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8536 (mmt180) REVERT: H 41 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7579 (p0) REVERT: H 68 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7753 (ttpp) REVERT: H 76 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8300 (mmt180) REVERT: I 41 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7470 (p0) REVERT: I 46 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8152 (ttmm) REVERT: I 68 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7702 (ttpp) REVERT: I 76 ARG cc_start: 0.8843 (mmt-90) cc_final: 0.8232 (mmt180) REVERT: J 41 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7584 (p0) REVERT: J 42 ASP cc_start: 0.8630 (p0) cc_final: 0.8408 (p0) REVERT: J 46 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8055 (mttp) REVERT: J 68 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7784 (ttpp) REVERT: J 110 SER cc_start: 0.8947 (t) cc_final: 0.8721 (p) REVERT: K 41 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.7545 (p0) REVERT: K 46 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8121 (ttmm) REVERT: K 68 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7849 (ttpp) REVERT: K 76 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8236 (mpt180) REVERT: K 81 ASP cc_start: 0.8639 (m-30) cc_final: 0.8384 (m-30) REVERT: K 83 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8453 (mmtt) REVERT: K 110 SER cc_start: 0.9001 (t) cc_final: 0.8790 (p) REVERT: K 141 SER cc_start: 0.8859 (m) cc_final: 0.8555 (m) REVERT: L 41 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7665 (p0) REVERT: L 46 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8155 (ttmm) REVERT: L 68 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7826 (ttpp) REVERT: L 76 ARG cc_start: 0.8814 (mmt-90) cc_final: 0.8378 (mmt180) REVERT: L 141 SER cc_start: 0.8868 (m) cc_final: 0.8575 (m) REVERT: M 41 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.7596 (p0) REVERT: M 46 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8012 (ttmm) REVERT: M 68 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7766 (ttpp) REVERT: M 76 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8246 (mmt180) REVERT: M 78 PHE cc_start: 0.8938 (m-80) cc_final: 0.8690 (m-80) REVERT: M 110 SER cc_start: 0.8964 (t) cc_final: 0.8759 (p) REVERT: M 141 SER cc_start: 0.8873 (m) cc_final: 0.8641 (m) REVERT: N 41 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.7590 (p0) REVERT: N 46 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8188 (ttmm) REVERT: N 68 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7796 (ttpp) REVERT: N 76 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8418 (mpt180) REVERT: O 41 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7590 (p0) REVERT: O 42 ASP cc_start: 0.8760 (p0) cc_final: 0.8453 (p0) REVERT: O 46 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8079 (ttmm) REVERT: O 68 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7852 (ttpp) REVERT: O 76 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8341 (mpt180) REVERT: O 141 SER cc_start: 0.8862 (m) cc_final: 0.8631 (m) REVERT: P 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7673 (p0) REVERT: P 46 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8110 (ttmm) REVERT: P 76 ARG cc_start: 0.8842 (mmt-90) cc_final: 0.8207 (mmt180) REVERT: P 110 SER cc_start: 0.8995 (t) cc_final: 0.8789 (p) REVERT: Q 41 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7480 (p0) REVERT: Q 46 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8143 (ttmm) REVERT: Q 68 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7766 (ttpp) REVERT: R 41 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7538 (p0) REVERT: R 68 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7750 (ttpp) REVERT: R 76 ARG cc_start: 0.8910 (mmt-90) cc_final: 0.8402 (mmt180) REVERT: R 81 ASP cc_start: 0.8620 (m-30) cc_final: 0.8342 (m-30) REVERT: R 141 SER cc_start: 0.8859 (m) cc_final: 0.8563 (m) REVERT: S 41 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7434 (p0) REVERT: S 46 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8041 (mttp) REVERT: S 68 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7736 (ttpp) REVERT: S 76 ARG cc_start: 0.8749 (mmt-90) cc_final: 0.8358 (mmt180) REVERT: S 83 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8442 (mmtt) REVERT: S 110 SER cc_start: 0.8996 (t) cc_final: 0.8781 (p) REVERT: T 41 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7525 (p0) REVERT: T 42 ASP cc_start: 0.8610 (p0) cc_final: 0.8405 (p0) REVERT: T 46 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8032 (mttm) REVERT: T 68 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7770 (ttpp) REVERT: T 76 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8390 (mmt180) REVERT: T 110 SER cc_start: 0.9056 (t) cc_final: 0.8794 (m) REVERT: T 141 SER cc_start: 0.8866 (m) cc_final: 0.8568 (m) REVERT: U 41 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7490 (p0) REVERT: U 46 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8088 (ttmm) REVERT: U 68 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7797 (ttpp) REVERT: U 76 ARG cc_start: 0.8906 (mmt-90) cc_final: 0.8549 (mmt180) REVERT: U 110 SER cc_start: 0.8967 (t) cc_final: 0.8723 (p) REVERT: V 41 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7475 (p0) REVERT: V 46 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8183 (ttmm) REVERT: V 68 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7755 (ttpp) REVERT: V 76 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.8349 (mmt-90) REVERT: V 110 SER cc_start: 0.8959 (t) cc_final: 0.8734 (p) REVERT: W 41 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7516 (p0) REVERT: W 46 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8114 (ttmm) REVERT: W 68 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7721 (ttpp) REVERT: X 41 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7452 (p0) REVERT: X 46 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8144 (ttmm) REVERT: X 68 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7805 (ttpp) REVERT: X 76 ARG cc_start: 0.8871 (mmt-90) cc_final: 0.8404 (mmt-90) REVERT: X 141 SER cc_start: 0.8867 (m) cc_final: 0.8570 (m) outliers start: 92 outliers final: 53 residues processed: 1018 average time/residue: 0.7339 time to fit residues: 890.9355 Evaluate side-chains 1032 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 955 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 3 SER Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 212 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 360 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 102 HIS C 102 HIS D 8 ASN E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN R 8 ASN S 8 ASN S 20 GLN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 62 HIS V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.092271 restraints weight = 323092.602| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.96 r_work: 0.2679 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 36312 Z= 0.112 Angle : 0.458 6.819 49104 Z= 0.254 Chirality : 0.036 0.123 5112 Planarity : 0.003 0.035 6480 Dihedral : 12.943 179.817 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.84 % Favored : 97.82 % Rotamer: Outliers : 2.34 % Allowed : 26.23 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.41 (0.12), residues: 4320 helix: 4.46 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.34 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 19 TYR 0.016 0.001 TYR I 37 PHE 0.012 0.002 PHE R 38 TRP 0.006 0.001 TRP N 90 HIS 0.006 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (36312) covalent geometry : angle 0.45755 / 0.25 (49104) hydrogen bonds : bond 0.04487 / 2.99 ( 2640) hydrogen bonds : angle 3.17305 / 2.30 ( 7776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 995 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8057 (p0) cc_final: 0.7020 (p0) REVERT: A 42 ASP cc_start: 0.8306 (p0) cc_final: 0.8048 (p0) REVERT: A 46 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7687 (mttp) REVERT: A 68 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7493 (ttpp) REVERT: A 76 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8283 (mmt-90) REVERT: A 141 SER cc_start: 0.8716 (m) cc_final: 0.8477 (m) REVERT: B 8 ASN cc_start: 0.8961 (t0) cc_final: 0.8474 (t0) REVERT: B 41 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.6905 (p0) REVERT: B 46 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7631 (mttp) REVERT: B 68 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7589 (ttpt) REVERT: B 110 SER cc_start: 0.8852 (t) cc_final: 0.8588 (p) REVERT: C 8 ASN cc_start: 0.8866 (t0) cc_final: 0.8468 (t0) REVERT: C 41 ASP cc_start: 0.8066 (p0) cc_final: 0.7246 (p0) REVERT: C 46 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7686 (mttp) REVERT: C 110 SER cc_start: 0.8918 (t) cc_final: 0.8685 (p) REVERT: C 141 SER cc_start: 0.8699 (m) cc_final: 0.8463 (m) REVERT: D 41 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.6773 (p0) REVERT: D 46 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7639 (mttp) REVERT: D 68 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7404 (ttpp) REVERT: D 76 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8385 (mmt180) REVERT: D 141 SER cc_start: 0.8685 (m) cc_final: 0.8449 (m) REVERT: E 41 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.6941 (p0) REVERT: E 46 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7648 (mttp) REVERT: E 68 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7544 (ttpp) REVERT: E 76 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8512 (mpt180) REVERT: E 110 SER cc_start: 0.8884 (t) cc_final: 0.8627 (p) REVERT: F 41 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7036 (p0) REVERT: F 46 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7603 (mttp) REVERT: F 68 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7416 (ttpp) REVERT: G 41 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7240 (p0) REVERT: G 46 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7705 (mttp) REVERT: G 76 ARG cc_start: 0.8859 (mmt-90) cc_final: 0.8488 (mmt180) REVERT: G 141 SER cc_start: 0.8715 (m) cc_final: 0.8484 (m) REVERT: H 41 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7185 (p0) REVERT: H 68 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7604 (ttpp) REVERT: H 76 ARG cc_start: 0.8754 (mmt-90) cc_final: 0.8320 (mmt180) REVERT: I 41 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.6881 (p0) REVERT: I 46 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7659 (mttp) REVERT: I 68 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7369 (ttpp) REVERT: I 76 ARG cc_start: 0.8694 (mmt-90) cc_final: 0.8324 (mmt180) REVERT: J 8 ASN cc_start: 0.8960 (t0) cc_final: 0.8517 (t0) REVERT: J 41 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7102 (p0) REVERT: J 42 ASP cc_start: 0.8266 (p0) cc_final: 0.8036 (p0) REVERT: J 46 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7737 (mttp) REVERT: J 68 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7475 (ttpp) REVERT: J 110 SER cc_start: 0.8828 (t) cc_final: 0.8595 (p) REVERT: K 41 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.6853 (p0) REVERT: K 46 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7625 (mttp) REVERT: K 68 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7839 (ttpm) REVERT: K 76 ARG cc_start: 0.8587 (mmt-90) cc_final: 0.8171 (mpt180) REVERT: K 81 ASP cc_start: 0.8599 (m-30) cc_final: 0.8274 (m-30) REVERT: K 83 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8355 (mmtt) REVERT: K 110 SER cc_start: 0.8899 (t) cc_final: 0.8659 (p) REVERT: K 141 SER cc_start: 0.8688 (m) cc_final: 0.8445 (m) REVERT: L 41 ASP cc_start: 0.7945 (p0) cc_final: 0.7077 (p0) REVERT: L 46 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7638 (mttp) REVERT: L 68 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7773 (ttpm) REVERT: L 76 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.8254 (mmt-90) REVERT: L 141 SER cc_start: 0.8702 (m) cc_final: 0.8475 (m) REVERT: M 41 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.6912 (p0) REVERT: M 46 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7707 (mttp) REVERT: M 68 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7508 (ttpp) REVERT: M 76 ARG cc_start: 0.8812 (mmt-90) cc_final: 0.8362 (mmt180) REVERT: M 78 PHE cc_start: 0.8880 (m-80) cc_final: 0.8616 (m-80) REVERT: M 110 SER cc_start: 0.8835 (t) cc_final: 0.8586 (p) REVERT: M 141 SER cc_start: 0.8785 (m) cc_final: 0.8581 (m) REVERT: N 41 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7132 (p0) REVERT: N 46 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7663 (mttp) REVERT: N 68 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7773 (ttpm) REVERT: N 76 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8222 (mmt180) REVERT: N 141 SER cc_start: 0.8713 (m) cc_final: 0.8468 (m) REVERT: O 41 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7215 (p0) REVERT: O 42 ASP cc_start: 0.8364 (p0) cc_final: 0.8111 (p0) REVERT: O 46 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7756 (mttp) REVERT: O 68 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7565 (tmmt) REVERT: O 76 ARG cc_start: 0.8749 (mmt-90) cc_final: 0.8331 (mpt180) REVERT: O 141 SER cc_start: 0.8753 (m) cc_final: 0.8551 (m) REVERT: P 41 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.6936 (p0) REVERT: P 46 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7714 (mttp) REVERT: P 76 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8308 (mmt180) REVERT: P 110 SER cc_start: 0.8883 (t) cc_final: 0.8629 (p) REVERT: Q 41 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.6965 (p0) REVERT: Q 46 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7680 (mttp) REVERT: Q 68 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7571 (ttpp) REVERT: R 41 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7152 (p0) REVERT: R 46 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7775 (mttp) REVERT: R 68 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7528 (ttpp) REVERT: R 76 ARG cc_start: 0.8819 (mmt-90) cc_final: 0.8356 (mmt180) REVERT: R 81 ASP cc_start: 0.8617 (m-30) cc_final: 0.8259 (m-30) REVERT: R 141 SER cc_start: 0.8702 (m) cc_final: 0.8453 (m) REVERT: S 41 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.6937 (p0) REVERT: S 46 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7660 (mttp) REVERT: S 68 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7527 (ttpp) REVERT: S 76 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8325 (mmt180) REVERT: S 110 SER cc_start: 0.8859 (t) cc_final: 0.8608 (p) REVERT: T 41 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.6859 (p0) REVERT: T 46 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7707 (mttp) REVERT: T 68 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7574 (ttpp) REVERT: T 76 ARG cc_start: 0.8795 (mmt-90) cc_final: 0.8411 (mmt180) REVERT: T 83 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8420 (mmtt) REVERT: T 141 SER cc_start: 0.8723 (m) cc_final: 0.8492 (m) REVERT: U 41 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.6995 (p0) REVERT: U 46 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7652 (mttp) REVERT: U 68 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7455 (ttpp) REVERT: U 76 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: U 110 SER cc_start: 0.8854 (t) cc_final: 0.8560 (p) REVERT: V 41 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.6975 (p0) REVERT: V 46 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7658 (mttp) REVERT: V 68 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7455 (ttpp) REVERT: V 76 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8346 (mmt180) REVERT: V 110 SER cc_start: 0.8881 (t) cc_final: 0.8632 (p) REVERT: V 141 SER cc_start: 0.8761 (m) cc_final: 0.8537 (m) REVERT: W 41 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7068 (p0) REVERT: W 46 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7663 (mttp) REVERT: W 68 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7419 (ttpp) REVERT: W 110 SER cc_start: 0.8895 (t) cc_final: 0.8654 (p) REVERT: W 141 SER cc_start: 0.8689 (m) cc_final: 0.8446 (m) REVERT: X 41 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7040 (p0) REVERT: X 46 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7679 (mttp) REVERT: X 68 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7501 (ttpp) REVERT: X 76 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8377 (mpt180) REVERT: X 141 SER cc_start: 0.8732 (m) cc_final: 0.8499 (m) outliers start: 63 outliers final: 16 residues processed: 1008 average time/residue: 0.7377 time to fit residues: 886.4172 Evaluate side-chains 982 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 943 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain X residue 41 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 375 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 chunk 305 optimal weight: 8.9990 chunk 236 optimal weight: 0.0000 chunk 308 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 260 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 102 HIS C 102 HIS D 8 ASN E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN K 8 ASN K 102 HIS L 8 ASN M 8 ASN M 62 HIS N 8 ASN O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 8 ASN Q 102 HIS R 8 ASN R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 62 HIS V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.117860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094482 restraints weight = 303759.594| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.93 r_work: 0.2707 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 36312 Z= 0.107 Angle : 0.451 5.680 49104 Z= 0.249 Chirality : 0.035 0.121 5112 Planarity : 0.003 0.032 6480 Dihedral : 12.905 179.585 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.82 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 26.62 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.56 (0.12), residues: 4320 helix: 4.55 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.26 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 87 TYR 0.016 0.001 TYR P 134 PHE 0.012 0.002 PHE E 38 TRP 0.006 0.000 TRP N 90 HIS 0.006 0.001 HIS I 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (36312) covalent geometry : angle 0.45145 / 0.25 (49104) hydrogen bonds : bond 0.04155 / 2.77 ( 2640) hydrogen bonds : angle 3.12829 / 2.27 ( 7776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 956 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7893 (p0) cc_final: 0.7100 (p0) REVERT: A 42 ASP cc_start: 0.8182 (p0) cc_final: 0.7971 (p0) REVERT: A 68 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7432 (ttpp) REVERT: A 76 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8307 (mmt180) REVERT: A 110 SER cc_start: 0.8878 (t) cc_final: 0.8661 (p) REVERT: A 141 SER cc_start: 0.8747 (m) cc_final: 0.8519 (m) REVERT: B 41 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.6849 (p0) REVERT: B 46 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7632 (mttp) REVERT: B 110 SER cc_start: 0.8854 (t) cc_final: 0.8589 (p) REVERT: C 8 ASN cc_start: 0.8873 (t0) cc_final: 0.8481 (t0) REVERT: C 41 ASP cc_start: 0.7981 (p0) cc_final: 0.7131 (p0) REVERT: C 46 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7661 (mttp) REVERT: C 110 SER cc_start: 0.8916 (t) cc_final: 0.8680 (p) REVERT: D 41 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.6785 (p0) REVERT: D 68 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7525 (ttpp) REVERT: D 76 ARG cc_start: 0.8769 (mmt-90) cc_final: 0.8395 (mmt180) REVERT: D 141 SER cc_start: 0.8699 (m) cc_final: 0.8485 (m) REVERT: E 41 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.6808 (p0) REVERT: E 46 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7621 (mttp) REVERT: E 68 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7571 (ttpp) REVERT: E 76 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.8418 (mmt180) REVERT: E 110 SER cc_start: 0.8870 (t) cc_final: 0.8613 (p) REVERT: F 41 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.6971 (p0) REVERT: F 68 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7533 (ttpp) REVERT: G 41 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7180 (p0) REVERT: G 46 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7663 (mttp) REVERT: G 68 LYS cc_start: 0.8083 (ttpm) cc_final: 0.7843 (ttpt) REVERT: G 76 ARG cc_start: 0.8857 (mmt-90) cc_final: 0.8572 (mmt180) REVERT: H 41 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.6970 (p0) REVERT: H 68 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7634 (ttpp) REVERT: H 76 ARG cc_start: 0.8755 (mmt-90) cc_final: 0.8237 (mmt180) REVERT: H 110 SER cc_start: 0.8904 (t) cc_final: 0.8678 (p) REVERT: I 41 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.6801 (p0) REVERT: I 46 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7587 (mttp) REVERT: I 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7481 (ttpp) REVERT: I 76 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8422 (mpt180) REVERT: I 110 SER cc_start: 0.8860 (t) cc_final: 0.8647 (p) REVERT: J 8 ASN cc_start: 0.8954 (t0) cc_final: 0.8501 (t0) REVERT: J 41 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7131 (p0) REVERT: J 46 LYS cc_start: 0.8071 (ttpp) cc_final: 0.7696 (mttp) REVERT: J 68 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7485 (ttpp) REVERT: J 110 SER cc_start: 0.8828 (t) cc_final: 0.8588 (p) REVERT: K 41 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.6704 (p0) REVERT: K 46 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7629 (mttp) REVERT: K 68 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7843 (ttpm) REVERT: K 76 ARG cc_start: 0.8581 (mmt-90) cc_final: 0.8195 (mpt180) REVERT: K 81 ASP cc_start: 0.8576 (m-30) cc_final: 0.8225 (m-30) REVERT: K 110 SER cc_start: 0.8900 (t) cc_final: 0.8658 (p) REVERT: K 141 SER cc_start: 0.8705 (m) cc_final: 0.8477 (m) REVERT: L 41 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7060 (p0) REVERT: L 68 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7819 (ttpm) REVERT: L 76 ARG cc_start: 0.8687 (mmt-90) cc_final: 0.8292 (mpt180) REVERT: M 41 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.6815 (p0) REVERT: M 46 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7721 (mttp) REVERT: M 68 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7443 (ttpp) REVERT: M 76 ARG cc_start: 0.8822 (mmt-90) cc_final: 0.8368 (mmt180) REVERT: M 78 PHE cc_start: 0.8886 (m-80) cc_final: 0.8623 (m-80) REVERT: M 110 SER cc_start: 0.8824 (t) cc_final: 0.8576 (p) REVERT: N 41 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7158 (p0) REVERT: N 46 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7637 (mttp) REVERT: N 68 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7774 (ttpm) REVERT: N 76 ARG cc_start: 0.8651 (mmt-90) cc_final: 0.8368 (mpt180) REVERT: N 110 SER cc_start: 0.8876 (t) cc_final: 0.8639 (p) REVERT: N 141 SER cc_start: 0.8740 (m) cc_final: 0.8521 (m) REVERT: O 41 ASP cc_start: 0.7901 (p0) cc_final: 0.7115 (p0) REVERT: O 42 ASP cc_start: 0.8269 (p0) cc_final: 0.8048 (p0) REVERT: O 46 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7704 (mttp) REVERT: O 68 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7510 (ttpp) REVERT: O 76 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8334 (mpt180) REVERT: O 110 SER cc_start: 0.8862 (t) cc_final: 0.8644 (p) REVERT: P 41 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.6950 (p0) REVERT: P 46 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7686 (mttp) REVERT: P 76 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8428 (mpt180) REVERT: P 110 SER cc_start: 0.8883 (t) cc_final: 0.8629 (p) REVERT: Q 41 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7039 (p0) REVERT: Q 46 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7653 (mttp) REVERT: Q 68 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7550 (ttpp) REVERT: Q 110 SER cc_start: 0.8904 (t) cc_final: 0.8686 (p) REVERT: R 41 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.6995 (p0) REVERT: R 46 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7701 (mttp) REVERT: R 68 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7557 (ttpp) REVERT: R 76 ARG cc_start: 0.8822 (mmt-90) cc_final: 0.8393 (mmt180) REVERT: R 81 ASP cc_start: 0.8599 (m-30) cc_final: 0.8238 (m-30) REVERT: R 141 SER cc_start: 0.8711 (m) cc_final: 0.8484 (m) REVERT: S 41 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.6907 (p0) REVERT: S 46 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7661 (mttp) REVERT: S 68 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7536 (ttpp) REVERT: S 76 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8327 (mmt180) REVERT: S 110 SER cc_start: 0.8875 (t) cc_final: 0.8634 (p) REVERT: T 41 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.6915 (p0) REVERT: T 46 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7684 (mttp) REVERT: T 68 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7507 (ttpp) REVERT: T 76 ARG cc_start: 0.8817 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: T 83 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8449 (mmtt) REVERT: T 141 SER cc_start: 0.8736 (m) cc_final: 0.8518 (m) REVERT: U 41 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.6959 (p0) REVERT: U 46 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7627 (mttp) REVERT: U 68 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7426 (ttpp) REVERT: U 76 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8553 (mmt180) REVERT: U 110 SER cc_start: 0.8885 (t) cc_final: 0.8591 (p) REVERT: V 41 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7006 (p0) REVERT: V 46 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7616 (mttp) REVERT: V 68 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7551 (ttpp) REVERT: V 76 ARG cc_start: 0.8751 (mmt-90) cc_final: 0.8416 (mpt180) REVERT: V 110 SER cc_start: 0.8902 (t) cc_final: 0.8647 (p) REVERT: V 141 SER cc_start: 0.8789 (m) cc_final: 0.8577 (m) REVERT: W 41 ASP cc_start: 0.7834 (p0) cc_final: 0.7030 (p0) REVERT: W 68 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7539 (ttpp) REVERT: W 110 SER cc_start: 0.8905 (t) cc_final: 0.8657 (p) REVERT: W 141 SER cc_start: 0.8707 (m) cc_final: 0.8496 (m) REVERT: X 41 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.6981 (p0) REVERT: X 68 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7425 (ttpp) REVERT: X 76 ARG cc_start: 0.8742 (mmt-90) cc_final: 0.8399 (mpt180) REVERT: X 110 SER cc_start: 0.8889 (t) cc_final: 0.8676 (p) REVERT: X 141 SER cc_start: 0.8749 (m) cc_final: 0.8535 (m) outliers start: 35 outliers final: 11 residues processed: 960 average time/residue: 0.7491 time to fit residues: 859.5474 Evaluate side-chains 963 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 931 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain X residue 41 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 406 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 102 HIS C 102 HIS D 8 ASN E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN I 102 HIS K 8 ASN K 102 HIS L 8 ASN M 8 ASN M 62 HIS M 102 HIS N 8 ASN O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 8 ASN Q 102 HIS R 8 ASN R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 62 HIS U 102 HIS V 8 ASN V 62 HIS V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.092848 restraints weight = 314213.799| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.96 r_work: 0.2683 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1473 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1477 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36312 Z= 0.114 Angle : 0.458 5.537 49104 Z= 0.253 Chirality : 0.036 0.125 5112 Planarity : 0.003 0.032 6480 Dihedral : 12.931 179.957 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.79 % Favored : 97.92 % Rotamer: Outliers : 1.70 % Allowed : 26.44 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.54 (0.12), residues: 4320 helix: 4.53 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.21 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 40 TYR 0.017 0.001 TYR P 134 PHE 0.012 0.002 PHE W 38 TRP 0.006 0.001 TRP N 90 HIS 0.006 0.001 HIS I 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (36312) covalent geometry : angle 0.45789 / 0.25 (49104) hydrogen bonds : bond 0.04471 / 2.97 ( 2640) hydrogen bonds : angle 3.12761 / 2.27 ( 7776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16532.06 seconds wall clock time: 281 minutes 26.19 seconds (16886.19 seconds total)